Cross reference for OBI classes, properties and dataproperties back to ToC

This section provides details for each class and property defined by OBI.

Classes

(S)-1-(4-bromoacetamidobenzyl)EDTAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_59055

A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration.
has super-classes
molecular entity c

1,1-dihydroxy-3-ethoxy-2-butanonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_59052

A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position.
has super-classes
molecular entity c

1M-Duo Infinium HD BeadChipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002006

A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis.
Source
http://www.illumina.com/technology/infinium_hd_assay.ilmn
Example
Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850
has super-classes
Illumina BeadChip c

293-T cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110028

A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication.
Source
IEDB
http://www.biotech.ist.unige.it/cldb/cl5008.html
has super-classes
immortal cell line c

2x2 factorial designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500015

a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
Source
PMID: 17561240
Example
PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
has super-classes
factorial design c

3' rapid amplification of cDNA endsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002092

A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 3' end of the mRNA.
Source
https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/3-race-system-for-rapid-amplification-of-cdna-ends.html
has super-classes
rapid amplification of cDNA ends c

3D structural organization datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001155

A measurement datum that describes the structural orientation of a material entity in 3D space.
Example
The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
has super-classes
measurement datum c
has sub-classes
PDB file c, PDB file chain c

3D structure determination assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600045

An assay that determines the 3-dimensional configuration of an input material.
Source
IEDB
Example
The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein.
is equivalent to
assay c and (has_specified_output op some 3D structural organization datum c)
has super-classes
assay c
has sub-classes
3D structure determination of bound complex assay c, 3D structure determining assay of a 3D B cell epitope:antibody complex c, 3D structure determining assay of a T cell epitope:MHC:TCR complex c, X-ray crystallography assay c, nuclear magnetic resonance 3D structure determination assay c, small-angle scattering assay c

3D structure determination of bound complex assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001145

A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration.
Source
IEDB
Example
Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody.
is equivalent to
3D structure determination assay c and (has_specified_output op some is about op some binding c)
has super-classes
binding assay c
3D structure determination assay c
has sub-classes
3D structure determining assay of a MHC:ligand complex c

3D structure determining assay of a 3D B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001721

A B cell epitope recognition assay that characterizes the 3D structure of an antibody / BCR with a ligand.
Source
IEDB
is equivalent to
assay measuring binding of a B cell epitope:antibody complex c and (has part op some 3D structure determination of bound complex assay c) and (has_specified_output op some 3D structural organization datum c)
has super-classes
3D structure determination assay c
assay measuring binding of a B cell epitope:antibody complex c
has sub-classes
NMR assay determining the 3D structure of a B cell epitope:antibody complex c, X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex c, electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex c, small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex c

3D structure determining assay of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002050

A MHC:ligand binding assay that uses a 3D structure determination of bound complex assay.
Source
IEDB
is equivalent to
assay measuring binding of a MHC:ligand complex c and (has part op some 3D structure determination of bound complex assay c) and (has_specified_output op some 3D structural organization datum c)
has super-classes
3D structure determination of bound complex assay c
assay measuring binding of a MHC:ligand complex c
has sub-classes
X-ray crystallography assay determining the 3D structure of a MHC:ligand complex c

3D structure determining assay of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001999

A T cell epitope recognition assay that uses a 3D structure determination of bound complex assay.
Source
IEDB
is equivalent to
assay measuring binding of a T cell epitope:MHC:TCR complex c and (has part op some 3D structure determination of bound complex assay c) and (has_specified_output op some 3D structural organization datum c)
has super-classes
3D structure determination assay c
assay measuring binding of a T cell epitope:MHC:TCR complex c
has sub-classes
X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex c

3H-thymidine assay measuring epitope specific proliferation of T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110180

A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay.
Source
IEDB
is equivalent to
in vitro assay measuring epitope specific proliferation of T cells c and (has part op some tritiated thymidine incorporation assay c)
has super-classes
in vitro assay measuring epitope specific proliferation of T cells c

454 Genome Sequence 20c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000689

is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
Example
PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
has super-classes
DNA sequencer c
is_manufactured_by op value Roche

454 Genome Sequencer FLXc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000702

is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
Source
adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
Example
PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10.
has super-classes
DNA sequencer c
is_manufactured_by op value Roche

5' rapid amplification of cDNA endsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002091

A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 5' end of the mRNA.
Source
https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/5-race-system-for-rapid-amplification-of-cdna-ends.html
has super-classes
rapid amplification of cDNA ends c
has sub-classes
5' RNA ligase mediated rapid amplification of cDNA ends c

5' RNA ligase mediated rapid amplification of cDNA endsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002093

A 5' rapid amplification pf cDNA ends that uses RNA ligase to add an RNA adapter oligonucleotide to intact 5' mRNA ends, allowing the amplification of cDNA only from full-length, capped mRNA.
Source
https://tools.thermofisher.com/content/sfs/manuals/cms_056070.pdf
has super-classes
5' rapid amplification of cDNA ends c

5'-adenylyl sulfatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_17709

An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups.
has super-classes
molecular entity c

5-bromo-2'-deoxyuridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_472552

A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.
has super-classes
molecular entity c

50% dissociation of binding temperature (Tm)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001566

A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound.
Source
IEDB
Example
Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated.
has super-classes
binding datum c
has measurement unit label op some temperature unit c

51 chromium assay measuring epitope specific T cell killingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110150

A T cell epitope specific killing assay performed in vitro that uses a chromium release assay.
Source
IEDB
is equivalent to
in vitro assay measuring epitope specific T cell killing c and (has part op some chromium release assay c)
has super-classes
in vitro assay measuring epitope specific T cell killing c

96-well neutralization assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000865

A serum neutralization of viral infectivity assay which done in a 96-well plate.
has super-classes
serum neutralization of viral infectivity assay c

a mating type (yeast)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001341

A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating.
has super-classes
biological sex c

A10-Analyzerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400005

A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells.
Source
http://www.apogeeflow.com/flow_cytometry_products.htm
has super-classes
flow cytometer analyzer c

A40-MiniFCMc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400006

A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus.
Source
http://www.apogeeflow.com/flow_cytometry_products.htm
has super-classes
flow cytometer analyzer c

AB SOLiD Systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000696

is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
Source
Applied Biosystems
Example
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
has super-classes
DNA sequencer c
is_manufactured_by op value Applied Biosystems
has sub-classes
SOLiD 3 Plus System c, SOLiD 4 System c

ABI 377 automated sequencerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000691

is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
Source
Applied Biosystems
has super-classes
DNA sequencer c
is_manufactured_by op value Applied Biosystems

abstractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000315

A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
Example
The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
has super-classes
document part c
is about op some document c

access servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001551

A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service.
Source
PERSON: Matthew Brush
Example
A service that provides acess to a mass spectrometer.
has super-classes
service c

accessed material rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000949

is realized in a planned process where the bearer participates
Example
the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
has super-classes
role c

acclimatizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600011

A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment.
Source
CEBS, Biomaterial_branch
Example
placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress
has super-classes
exposure of material to environment c

acknowledgements sectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000324

Part of a publication that is about the contributions of people or institutions other than the authors.
Example
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
has super-classes
document part c

acquisitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600008

the planned process of gaining possession of a continuant
Source
IEDB
Example
Downloading a 3D structure from the PDB. Purchasing antibodies from sigma.
has super-classes
selection c
realizes op some concretizes op some selection criterion c
has_specified_output op some material entity c or information content entity c
has sub-classes
information acquisition c, material acquisition c

acquisition computerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000636

A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013
has super-classes
computer c
has function op some information processor function c

acrylamidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_28619

A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
has super-classes
molecular entity c

actin filament polymerizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0030041

Assembly of actin filaments by the addition of actin monomers to a filament.
has super-classes
biological_process c

actin polymerization-dependent cell motilityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0070358

A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell.
has super-classes
biological_process c

action specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000007

a directive information entity that describes an action the bearer will take
Source
OBI Plan and Planned Process branch
Example
Pour the contents of flask 1 into flask 2
has super-classes
directive information entity c

activated partial thromboplastin time (aPTT) assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000820

An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms.
Source
WEB:http://en.wikipedia.org/wiki/Partial_thromboplastin_time@2008/10/06
Example
PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent.
has super-classes
assay c
(has_specified_input op some blood serum specimen c) and (has_specified_output op some scalar measurement datum c and (is about op some blood coagulation c))

adaptive immune effector functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110016

A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience.
Source
IEDB
has super-classes
function c
inheres in op some T cell c or B cell c or immunoglobulin complex, circulating c
realized in op only adaptive immune response c
has sub-classes
effector T cell function c

adaptive immune receptorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110022

is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
Source
IEDB
is equivalent to
B cell receptor complex c or T cell receptor complex c or immunoglobulin complex, circulating c
has super-classes
protein complex c
has sub-classes
B cell receptor complex c, T cell receptor complex c, immunoglobulin complex, circulating c

adaptive immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0002250

An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
has super-classes
immune response c
has sub-classes
helper T cell enhancement of adaptive immune response c

adding a material entity into a targetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000274

is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Source
branch derived
Example
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is equivalent to
achieves_planned_objective op some adding material objective c
has super-classes
material combination c
realizes op some material to be added role c
realizes op some target of material addition role c
has_specified_output op some material entity c and (has role op some material to be added role c) and (located in op some material entity c and (has role op some target of material addition role c))
has sub-classes
adding substance to cell culture c, administering substance in vivo c, administration of material to specimen c, injection c

adding material objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000434

is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
Example
creating a mouse infected with LCM virus
has super-classes
material combination objective c

adding substance to cell culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600000

is process in which a material substance is added to a cell culture
Source
IEDB
Example
adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient
is equivalent to
(realizes op some material to be added role c) and (realizes op some target of material addition role c and (role of op some cultured cell population c))
has super-classes
adding a material entity into a target c
has_specified_input op some cultured cell population c
has_specified_output op some cultured cell population c
achieves_planned_objective op some adding material objective c
has sub-classes
experimental infection of cell culture c

addition of molecular labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600038

a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
Source
OBI developer call, 3-12-12
Example
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
has super-classes
material processing c
has_specified_input op some target of material addition c
has_specified_input op some molecular label c
has_specified_output op some molecular-labeled material c
achieves_planned_objective op some material transformation objective c
has sub-classes
non-specific labeling c, random primed DNA labeling c, specific labeling c

addition of molecular tracer functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000961

A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen.
Source
PERSON: Nicole Vasilevsky, Matthew Brush
Example
Immunohistochemical labeling of tissue sections by an autostainer staining system.
has super-classes
reagent application function c

adipose tissuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001013

Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
has super-classes
tissue c

adipose tissue specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002530

A specimen that is derived from adipose tissue.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some adipose tissue c))
has super-classes
specimen from organism c

adjuvant rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110092

Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response.
Source
IEDB
has super-classes
role c
inheres in op some material entity c
realized in op only biological_process c
has sub-classes
immunologic adjuvant role c

administering substance in vivoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600007

A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
Source
IEDB
Example
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
is equivalent to
(realizes op some material to be added role c) and (realizes op some target of material addition role c and (role of op some organism c or material anatomical entity c))
has super-classes
adding a material entity into a target c
has_specified_input op some organism c
has_specified_output op some organism c
achieves_planned_objective op some adding material objective c
has_specified_output op max 1
has sub-classes
administration in vivo with infectious agent c, intradermal injection c, intramuscular injection c, intranasal mucosal administration c, intraperitoneal administration c, intravenous injection c, oral administration c, passive immunization c, pathogen challenge c, subcutaneous injection c, vaccination c

administration in vivo with infectious agentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110007

is an administration of an infectious agent to a host organism
Source
IEDB
has super-classes
administering substance in vivo c
realizes op some material to be added role c and (role of op some infectious agent c)

administration of material to specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000995

The directed combination of a material entity with a specimen.
Source
Bjoern Peters
Example
Staining cells in a tissue slice with a dye.
has super-classes
adding a material entity into a target c
realizes op some target of material addition role c and (role of op some specimen c)

adrenal glandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002369

Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
has super-classes
material anatomical entity c

adrenal gland specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002522

A specimen that is derived from adrenal gland.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some adrenal gland c))
has super-classes
specimen from organism c

adverse event triggerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000310

revisit?
Source
OBI branch derived
has super-classes
conditional specification c

affinity columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000533

An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094
has super-classes
chromatography column c

agar stab specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000981

a specimen that is output of a process that cell culture inoculated into agar for long term storage.
Source
MO_971 agar_stab
is equivalent to
is_specified_output_of op some agar stab storage c and (has_specified_input op some has role op some specimen role c)
has super-classes
specimen with known storage state c
is disjoint with
frozen specimen c, paraffin specimen c, lyophilized specimen c, fresh specimen c

agar stab storagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001003

a storage process with input cell culture and agar and output agar stab for long time storage
need to specify that agar is one of input for this process
Source
UPenn Group
has super-classes
storage c
has_specified_input op some cultured cell population c
achieves_planned_objective op some material maintenance objective c

agarose gelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000439

a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
Source
GROUP: OBI Biomaterial Branch
Example
Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
has super-classes
processed material c
is_specified_output_of op some polymerization c

agarose gel electrophoresis systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001134

A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
Source
http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis
has super-classes
electrophoresis system c

agec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000011

A time quality inhering in a bearer by virtue of how long the bearer has existed.
has super-classes
quality of a single physical entity c

age measurement assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001158

An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
Source
OBI group
has super-classes
assay c
has_specified_output op some age measurement datum c

age measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001167

A time measurement datum that is the result of measurement of age of an organism
Source
MO_178 Age
has super-classes
time measurement datum c
is quality measurement of op some age c
is_specified_output_of op some age measurement assay c
has sub-classes
age since birth measurement datum c, age since coitus measurement datum c, age since eclosion measurement datum c, age since egg laying measurement datum c, age since fertilization measurement datum c, age since germination measurement datum c, age since hatching measurement datum c, age since planting measurement datum c, age since sowing measurement datum c

age since birth measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001169

An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
Source
MO_710 birth
has super-classes
age measurement datum c

age since coitus measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001165

An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
Source
MO_783 coitus
has super-classes
age measurement datum c

age since eclosion measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001163

An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
Source
MO_876 eclosion
has super-classes
age measurement datum c

age since egg laying measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001159

An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
Source
MO_767 egg laying
has super-classes
age measurement datum c

age since fertilization measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001168

An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
Source
MO_701 fertilization
has super-classes
age measurement datum c

age since germination measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001161

An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
Source
MO_590 germination
has super-classes
age measurement datum c

age since hatching measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001157

An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
Source
MO_745 hatching
has super-classes
age measurement datum c

age since planting measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001156

An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
Source
MO_495 planting
has super-classes
age measurement datum c

age since sowing measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001164

An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
Source
MO_748 sowing
has super-classes
age measurement datum c

agglomerative hierarchical clusteringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200154

An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining.
Source
PERSON: Elisabetta Manduchi
has super-classes
hierarchical clustering c
has sub-classes
average linkage hierarchical clustering c, complete linkage hierarchical clustering c, single linkage hierarchical clustering c

Alexa Fluor 532c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_51756

An organosulfonic acid that has formula C34H33N3O11S2.
has super-classes
molecular label c
has role op some molecular label role c

Alexa Fluor 546c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_51760

An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3.
has super-classes
molecular label c
has role op some molecular label role c

Alexa Fluor 555c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_52673

A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.
has super-classes
molecular label c
has role op some molecular label role c

algorithmc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000064

A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Source
OBI_0000270
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
Example
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has super-classes
plan specification c
has sub-classes
sequence annotation algorithm c, sequence assembly algorithm c, software interpreter c

alivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001421

A viability quality inhering in a bearer by virtue of the bearer's condition before death.
has super-classes
quality of a single physical entity c

all pairs designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001440

A study design in which all specimens are compared to every other specimen.
Source
MO_565 all_pairs
has super-classes
study design c

allele informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001352

a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
Source
MO_58 Allele
Example
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
has super-classes
genetic alteration information c
(part of op some genotype information c) and (is about op some region c)
has sub-classes
wild type allele information c

allergenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110201

A material entity bearing the disposition to cause an allergic reaction
Source
IEDB
Example
Birch pollen is an allergen
is equivalent to
material entity c and (bearer of op some disposition to cause an allergic reaction c)
has super-classes
material entity c

allergic reactionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110011

an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen)
Source
IEDB
has super-classes
pathologic process c
realizes op some disposition to cause an allergic reaction c

allergyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110049

is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect
Source
IEDB
has super-classes
disease c

allotransplantationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000057

is the transplantation of organs between members of the same species.
Source
OBI branch derived
has super-classes
transplantation c

alpha mating type (yeast)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001344

A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids.
has super-classes
biological sex c

alpha-beta T cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000789

A T cell that expresses an alpha-beta T cell receptor complex.
has super-classes
T cell c
has sub-classes
CD4-positive, alpha-beta T cell c, CD8-positive, alpha-beta T cell c, mature NK T cell c

ambidextrous handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0002204

Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
has super-classes
handedness c

amino acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33709

A carboxylic acid containing one or more amino groups.
has super-classes
molecular entity c

Amniotac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_32524

has super-classes
Tetrapoda c
has sub-classes
Gallus gallus c, Mammalia c

amniotic fluidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000173

Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
has super-classes
organism substance c

amniotic fluid specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002500

A specimen that is derived from amniotic fluid.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some amniotic fluid c))
has super-classes
specimen from organism c

Amnis ImageStreamc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400054

The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow. It has both components, an Image cytometer and a flow cytometer.
Source
http://www.amnis.com/
has super-classes
multispectral imaging flow cytometer c
has part op some flow cytometer c
has part op some image cytometer c

amplification of intermethylated sites (AIMS) assay c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001685

amplification of intermethylated sites (AIMS) is an assay appropriate for genome-wide estimates of DNA methylation and the discovery of specific methylated sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences.
Source
PMID: 18987810
Example
Analysis of DNA methylation by amplification of intermethylated sites (AIMS).PMID:18987810
is equivalent to
(assay c and (has_specified_input op some high molecular weight DNA extract c) and (has_specified_output op some data item c and (is about op some regulation of DNA methylation c))) and (achieves_planned_objective op some epigenetic modification identification objective c)
has super-classes
DNA methylation profiling assay c

amplified DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000809

DNA that has been produced in an enzymatic amplification process
Source
Alan Ruttenberg
Example
Amplied DNA created by PCR
is equivalent to
deoxyribonucleic acid c and (is_specified_output_of op some enzymatic amplification c)
has super-classes
deoxyribonucleic acid c
processed material c
has sub-classes
PCR product c

analog-to-digital converterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400007

An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal.
Source
http://en.wiktionary.org/wiki/Analog-to-Digital_Converter
Example
The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection.
has super-classes
device c
has function op some signal conversion function c

analyte assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000443

An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
Source
PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
Example
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
is equivalent to
achieves_planned_objective op some analyte measurement objective c
has super-classes
assay c
realizes op some analyte role c
has_specified_output op some measurement datum c
has sub-classes
DNA methylation profiling assay c, RNA-binding protein immunoprecipitation array profiling assay c, RNAi profiling by array assay c, RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay c, Southern blot analysis c, analytical chromatography c, clinical chemistry assay c, cross-linking immunoprecipitation high-throughput sequencing assay c, cytometric bead array assay c, detection of specific nucleic acid polymers with complementary probes c, enzyme-linked immunosorbent assay c, genotyping assay c, human antithrombin-III (AT-III) in blood assay c, immunoblot assay c, immunoprecipitation assay c, measuring glucose concentration in blood serum c, microarray assay c, northern blot analysis c, proteomic profiling by array assay c, reporter cell line analyte detection bioassay c, serum neutralization of viral infectivity assay c, transcription profiling assay c, translation profiling assay c, viral hemagglutination assay c

analyte measurement objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000437

an assay objective to determine the presence or concentration of an analyte in the evaluant
Source
PPPB branch
Example
The objective to measure the concentration of glucose in a blood sample
has super-classes
assay objective c

analyte rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000275

A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role
Source
OBI
Example
Glucose in blood (measured in an assay to determine the concentration of glucose).
has super-classes
role c
role of op some molecular entity c or atom c
realized in op only analyte assay c

analytical balancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001104

A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy.
Source
http://en.wikipedia.org/wiki/Weighing_scale
has super-classes
balance c

analytical chromatographyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001630

An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material.
Source
IEDB
Example
Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column.
is equivalent to
analyte assay c and ((realizes op some function c and (inheres in op some chromatography column c)) and (has_specified_input op some chromatography column c)) and ((realizes op some reagent role c and (inheres in op some chromatography consumable c)) and (has_specified_input op some chromatography consumable c))
has super-classes
analyte assay c
has sub-classes
high performance liquid chromotography assay c

analytical cytology data filec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000210

A digital entity intended to capture data in analytical cytology domain.
Source
group:Flow Cytometry community
Example
FCS file, ACS file, foo.fcs, foo.asc
has super-classes
information content entity c

anatomical clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000477

Anatomical group that has its parts adjacent to one another.
has super-classes
material entity c
has sub-classes
caudate nucleus c, cerebral cortex c, putamen c, tibial nerve c

aneuploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001385

A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes.
has super-classes
ploidy c

angiographc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001044

A device that records the patterns of pulse waves inside blood vessels.
Source
http://medical-dictionary.thefreedictionary.com/angiograph
has super-classes
measurement device c
has function op some record function c
has function op some measure function c

animal cagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400171

a processed material which has the function to define a bounded habitat which is amenable to keeping animals.
Source
OBI biomaterial branch
Example
PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
has super-classes
container c
has function op some contain function c

animal care protocolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000715

An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes
Source
Bjoern Peters
Example
Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
has super-classes
protocol c
has sub-classes
rodent care protocol c

animal euthanizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000919

A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject
may later be refined with more specific list of organisms
Source
Melissa Haendel
Example
Rats were euthanized with CO2
has super-classes
killing c
has_specified_input op some Vertebrata <Metazoa> c
has sub-classes
asphyxiation c, cervical dislocation c, decapitation c, electrocution c, intentional overdosing c

animal feedingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000694

animal feeding is a process in which animals are provided with food
Source
branch derived
Example
giving crickets to a snake.
has super-classes
planned process c
realizes op some feed role c
has_specified_input op some organism c
has_specified_output op some organism c

anion exchange columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000584

An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095
has super-classes
ion exchange column c

anion trap columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000562

An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277
has super-classes
trap column c

ANOVAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200201

ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal.
has super-classes
data transformation c

anterior toc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001632

A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity.
has super-classes
relational spatial quality c

antibody binding detection by fluorescence quenchingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001635

A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope).
Source
IEDB
Example
The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844).
has super-classes
fluorescence quenching binding assay c
(realizes op some evaluant role c and (inheres in op some immunoglobulin complex, circulating c)) and (has_specified_input op some immunoglobulin complex, circulating c)
has part op some fluorescence detection assay c
has_specified_output op some is about op some binding c

antibody cross-blocking assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001699

A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites.
Source
IEDB
Example
Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format.
has super-classes
competitive inhibition of binding assay c
(realizes op some evaluant role c and (inheres in op some immunoglobulin complex, circulating c)) and (has_specified_input op some immunoglobulin complex, circulating c)
has_specified_input op some immunoglobulin complex, circulating c and (has role op some positive reference substance role c)

antibody-dependent cellular cytotoxicityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0001788

Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells.
has super-classes
biological_process c
has sub-classes
B cell epitope specific antibody-dependent cellular cytotoxicity c

anticoagulant tube storage of blood specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000819

Storage of a blood specimen in a tube with anticoagulant
has super-classes
storage c
(has_specified_input op some blood serum specimen c) and (has_specified_output op some anticoagulant-containing test tube c and (surrounded by op some blood serum specimen c))

anticoagulant-containing test tubec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000784

A 'blue top' test tube that contains anticoagulant for storing blood specimens'
has super-classes
test tube c
surrounded by op some has part op some has grain op some sodium citrate dihydrate c

antigenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110034

is a material entity that has the antigen role
Source
IEDB
is equivalent to
has role op some assay antigen role c
has super-classes
material entity c

antigen bindingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0003823

Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
has super-classes
process c
has sub-classes
peptide antigen binding c

antigen inhibition assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001701

A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand.
Source
IEDB
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c
has_specified_input op some material entity c and (has role op some positive reference substance role c)

antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001638

A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay.
Source
IEDB
has super-classes
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c
has_specified_input op some material entity c and (has role op some positive reference substance role c)
has_specified_output op some equilibrium dissociation constant (KD) approximated by IC50 c
has_specified_output op some has measurement unit label op value nanomolar

antigen presentation functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110085

a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface.
Source
IEDB
has super-classes
function c
inheres in op some cell c and (has part op some MHC protein complex c)

antigen processing and presentationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0019882

The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
has super-classes
biological_process c

antigen rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000237

Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response
Source
OBI
has super-classes
role c
realized in op only immune response c

antithrombin-IIIc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000003252

A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof.
has super-classes
protein c

antithrombin-III (AT-III) berichrome assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000805

An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard
Source
WEB:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
has super-classes
human antithrombin-III (AT-III) in blood assay c
(has_specified_output op some scalar measurement datum c) and (has participant op some Berichrom(r) Antithrombin III (A) Kit c) and (has_specified_output op exactly 1)

aortac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000947

The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation
has super-classes
material anatomical entity c

aorta specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002542

A specimen that is derived from aorta.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some aorta c))
has super-classes
specimen from organism c

APOLLO consolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000483

The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application.
Source
WEB:<http://www.tecmag.com/apollo.htm>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249
has super-classes
tecmag NMR console c

Arabidopsis thalianac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_3702

has super-classes
Eukaryota c

arc lampc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400009

Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point.
Source
http://en.wikipedia.org/wiki/Arc_lamp
Example
The Jablochkoff Candle
has super-classes
light source c

Archaeac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2157

has super-classes
organism c

argon ion laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400010

An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes.
Source
John Quinn
http://en.wikipedia.org/wiki/Laser#Gas_lasers
Example
argon ion laser in a cytometer
has super-classes
ion laser c

arithmetic mean calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200079

An arithmetic mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
Source
PERSON: James Malone
PERSON: Monnie McGee
has super-classes
averaging data transformation c
center calculation data transformation c
descriptive statistical calculation data transformation c
(has_specified_output op some center value c) and (achieves_planned_objective op some center calculation objective c)
(has_specified_output op some average value c) and (achieves_planned_objective op some averaging objective c)
achieves_planned_objective op some descriptive statistical calculation objective c

array based nucleic acid structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002036

An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray.
Source
OBI:0000870
Example
pmid:23580730
has super-classes
assay c
has sub-classes
micrococcal nuclease digestion followed by tiling array assay c

array image creationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001031

An image creation process that generate an image from the array.
Source
MO_929: image_acquisition
has super-classes
image creation c
has_specified_input op some microarray c
has_specified_output op some image c

array manufacturer rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001069

a manufacturer role which is played by the person or organization that manufactured the array
Source
MO_695 array_manufacturer
has super-classes
manufacturer role c
realized in op only manufacturing c and (has_specified_output op some microarray c)

array platform variation designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001252

A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
Source
MO_899 array_platform_variation_design
has super-classes
study design c
has part op some methodology testing objective c
has part op some study design independent variable c and (is about op some microarray platform c)

array scannerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400104

An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip
Source
GROUP: MGED Ontology
Example
GenePix 4200A, GenePix4000B
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

arrayerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400105

a device which deposits biological material onto a substrate in a defined pattern.
Source
MO_697 arrayer
Example
BioRobotics Microgrid II TAS, Affymetrix GMS 417
has super-classes
device c
has function op some transfer function c

artificially induced cell membrane lysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600027

a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate
Source
OBI branch derived
Example
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent.
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

artificially induced DNA repairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600032

a protocol application to repair damaged DNA molecules
Source
OBI branch derived
Example
the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

artificially induced methylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600039

A planned process of adding methyl groups to polymers
Source
OBI branch derived
Example
the use of enzymes to add methyl groups to DNA molecules
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

artificially induced nucleic acid hybridizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000253

Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
Source
OBI branch derived
Example
www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

artificially induced reverse transcriptionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600028

a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
Source
OBI branch derived
Example
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
has super-classes
material processing c
has_specified_input op some ribonucleic acid c
has_specified_input op some reverse transcriptase c
has_specified_output op some deoxyribonucleic acid c
achieves_planned_objective op some material transformation objective c

Ascomycotac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_4890

has super-classes
Opisthokonta c
has sub-classes
Schizosaccharomyces pombe c, saccharomyceta c

asphyxiationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302897

asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms.
Source
OBI branch
Example
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
has super-classes
animal euthanization c

assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000070

A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
Source
OBI branch derived
Example
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
is equivalent to
achieves_planned_objective op some assay objective c
has super-classes
planned process c
realizes op some evaluant role c
has_specified_input op some material entity c and (has role op some evaluant role c)
has_specified_output op some information content entity c and (is about op some material entity c and (has role op some evaluant role c))
has sub-classes
3D structure determination assay c, Bernoulli trial c, DNA replication timing by array assay c, DNA sequence feature detection c, DNA sequence variation detection c, NMR spectroscopy c, RNA protection assay c, activated partial thromboplastin time (aPTT) assay c, age measurement assay c, analyte assay c, array based nucleic acid structure mapping assay c, assay detecting IFN-gamma production c, assay for transposase-accessible chromatin using sequencing c, binding assay c, comet assay c, copy number variation profiling c, cytochalasin-induced inhibition of actin polymerization assay c, cytometry assay c, detection of molecular label c, efficacy of epitope intervention experiment c, epigenetic modification assay c, extracellular electrophysiology recording c, fluorescence detection assay c, gene dosage assay c, gene knock-down assay c, glucose tolerance test c, handedness assay c, hematology c, histology c, hydrogen/deuterium exchange assay c, imaging assay c, immune epitope assay c, immune response assay c, in container assay c, in live cell assay c, in live organism assay c, in situ hybridization c, in vivo intervention experiment c, infectious agent detection assay c, intra cellular electrophysiology recording c, longitudinal mass measurement assay c, mass measurement assay c, mass spectrometry assay c, metabolite profiling c, methylation-specific polymerase chain reaction c, organism identification assay c, performing a clinical assessment c, protein expression profiling c, protein-protein interaction detection c, prothrombin time assay c, radio immuno assay c, radioactivity detection c, real time polymerase chain reaction assay c, real time reverse-transcription polymerase chain reaction assay c, reporter gene assay c, reverse transcription polymerase chain reaction assay c, sequencing assay c, single-nucleotide-resolution nucleic acid structure mapping assay c, spectrolyse heparin antifactor-Xa assay c, substance detection c, survival assessment c, thrombin time assay c, tumor grading c, viral hemagglutination inhibition assay c
is disjoint with
planning c, data transformation c, information acquisition c

assay antigen rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110120

Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. see OBI_1110120 below
Source
IEDB
has super-classes
role c
realized in op only assay c

assay arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001865

A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
Source
Penn Group
has super-classes
device c
has function op some solid support function c
has sub-classes
Illumina BeadChip c, microarray c, nCounter Human V2 miRNA Expression array c

assay beadc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1000207

A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules.
Example
Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations.
has super-classes
processed material c

assay detecting IFN-gamma productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110207

an assay that determines information about the production of the cytokine interferon gamma
Source
IEDB
Example
An IFN-g ELISPOT is an assay detecting ifn-gamma production
is equivalent to
assay c and (has_specified_output op some measurement datum c and (is about op some interferon-gamma production c))
has super-classes
assay c

assay for transposase-accessible chromatin using sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002039

An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion.
Source
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, and Greenleaf WJ. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods
Example
Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766.
has super-classes
assay c

assay measuring a binding constant of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001709

A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant.
Source
IEDB
is equivalent to
assay measuring binding of a B cell epitope:antibody complex c and (has_specified_output op some binding constant c)
has super-classes
binding constant determination assay c
assay measuring binding of a B cell epitope:antibody complex c
has sub-classes
assay measuring the association constant [KA] of a B cell epitope:antibody complex c, assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, assay measuring the off rate [koff] of a B cell epitope:antibody complex c, assay measuring the on rate [kon] of a B cell epitope:antibody complex c

assay measuring a binding constant of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001553

A MHC:ligand binding assay that measures a binding constant.
Source
IEDB
is equivalent to
assay measuring binding of a MHC:ligand complex c and (has_specified_output op some binding constant c)
has super-classes
binding constant determination assay c
assay measuring binding of a MHC:ligand complex c
has sub-classes
assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex c, assay measuring the association constant [KA] of a MHC:ligand complex c, assay measuring the dissociation constant [KD] of a MHC:ligand complex c, assay measuring the half life of a MHC:ligand complex c, assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex c, assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c, assay measuring the off rate measurement [koff] of a MHC:ligand complex c

assay measuring a binding constant of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002059

A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant.
Source
IEDB
has super-classes
binding constant determination assay c
assay measuring binding of a T cell epitope:MHC:TCR complex c
has_specified_output op some binding constant c
has sub-classes
assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex c, assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex c, assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex c, assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex c

assay measuring B cell epitope specific biological activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001706

A B cell epitope recognition assay that detects biological activity.
Source
IEDB
is equivalent to
assay measuring binding of a B cell epitope:antibody complex c and (has_specified_output op some information content entity c and (is about op some process is result of op some immunoglobulin binding to epitope c))
has super-classes
assay measuring binding of a B cell epitope:antibody complex c
has sub-classes
biological activity assay measuring B cell epitope specific in vivo activity c, biological activity assay measuring epitope specific activation of additional immune response in vitro c, biological activity assay measuring epitope specific antigen inhibition of antibody activity c, biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation c, biological activity assay measuring epitope specific immunoglobulin-mediated neutralization c

assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110127

An immune epitope assay that detects B cell epitope recognition.
Source
IEDB
is equivalent to
immune epitope assay c and (has_specified_output op some information content entity c and (is about op some immunoglobulin binding to epitope c or (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
immune epitope assay c
has sub-classes
3D structure determining assay of a 3D B cell epitope:antibody complex c, assay measuring B cell epitope specific biological activity c, assay measuring a binding constant of a B cell epitope:antibody complex c, assay measuring qualitiative binding of a B cell epitope:antibody complex c

assay measuring binding of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110126

A MHC ligand assay that detects the binding of a ligand to an MHC molecule.
Source
IEDB
is equivalent to
MHC ligand assay c and (has_specified_output op some information content entity c and (is about op some MHC protein complex binding to ligand c and (not (process is result of op some antigen processing and presentation c))))
has super-classes
MHC ligand assay c
has sub-classes
3D structure determining assay of a MHC:ligand complex c, assay measuring a binding constant of a MHC:ligand complex c, assay measuring qualitiative binding of a MHC:ligand complex c

assay measuring binding of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110037

An immune epitope assay that detects T cell epitope recognition.
Source
IEDB
is equivalent to
immune epitope assay c and (has_specified_output op some information content entity c and (is about op some MHC:epitope complex binding to TCR c or (process is result of op some MHC:epitope complex binding to TCR c)))
has super-classes
immune epitope assay c
has sub-classes
3D structure determining assay of a T cell epitope:MHC:TCR complex c, assay measuring T cell epitope specific biological activity c, assay measuring a binding constant of a T cell epitope:MHC:TCR complex c, assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex c

assay measuring MHC ligand processing and presentationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110125

A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them.
Source
IEDB
is equivalent to
MHC ligand assay c and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some information content entity c and (is about op some MHC protein complex binding to ligand c and (process is result of op some antigen processing and presentation c)))
has super-classes
MHC ligand assay c
has sub-classes
Edman degradation assay measuring MHC ligand processing and presentation c, coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand c, mass spectrometry assay measuring MHC ligand processing and presentation c, monospecific T cell recognition assay measuring MHC ligand processing and presentation c

assay measuring qualitiative binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001703

A B cell epitope recognition assay that detects qualitative binding.
Source
IEDB
is equivalent to
assay measuring binding of a B cell epitope:antibody complex c and (has_specified_output op some information content entity c and (is about op some immunoglobulin binding to epitope c))
has super-classes
binding assay c
assay measuring binding of a B cell epitope:antibody complex c
has sub-classes
ELISA measuring binding of a B cell epitope:antibody complex c, ELISPOT assay measuring binding of a B cell epitope:antibody complex c, NMR assay measuring binding of a B cell epitope:antibody complex c, RIA measuring binding of a B cell epitope:antibody complex c, antigen inhibition assay measuring binding of a B cell epitope:antibody complex c, bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex c, biological activity assay measuring epitope specific hemagglutination inhibition c, calorimetry assay measuring binding of a B cell epitope:antibody complex c, chromatography assay measuring binding of a B cell epitope:antibody complex c, cross blocking assay measuring binding of a B cell epitope:antibody complex c, electron microscopy assay measuring binding of a B cell epitope:antibody complex c, flow cytometry assay measuring binding of a B cell epitope:antibody complex c, hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complex c, immuno staining assay measuring binding of a B cell epitope:antibody complex c, immunoblot assay measuring binding of a B cell epitope:antibody complex c, immunoprecipitation assay measuring binding of a B cell epitope:antibody complex c, mass spectrometry assay measuring binding of a B cell epitope:antibody complex c, microarray assay measuring binding of a B cell epitope:antibody complex c, phage display assay measuring binding of a B cell epitope:antibody complex c, plasmon resonance assay measuring binding of a B cell epitope:antibody complex c, quenching assay measuring binding of a B cell epitope:antibody complex c

assay measuring qualitiative binding of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002072

A MHC:ligand binding assay that detects qualitative binding.
Source
IEDB
has super-classes
assay measuring binding of a MHC:ligand complex c
has sub-classes
cell bound MHC binding assay measuring binding of a MHC:ligand complex c, cell lysate MHC binding assay measuring binding of a MHC:ligand complex c, purified MHC binding assay measuring binding of a MHC:ligand complex c

assay measuring qualitiative binding of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110124

A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR.
Source
IEDB
is equivalent to
assay measuring binding of a T cell epitope:MHC:TCR complex c and (has_specified_output op some information content entity c and (is about op some MHC:epitope complex binding to TCR c))
has super-classes
binding assay c
assay measuring binding of a T cell epitope:MHC:TCR complex c
has sub-classes
flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex c

assay measuring T cell epitope specific biological activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002055

A T cell epitope recognition assay that detects biological activity.
Source
IEDB
is equivalent to
assay measuring binding of a T cell epitope:MHC:TCR complex c and (has_specified_output op some information content entity c and (is about op some process is result of op some MHC:epitope complex binding to TCR c))
has super-classes
assay measuring binding of a T cell epitope:MHC:TCR complex c
has sub-classes
biological activity assay measuring T cell epitope specific in vivo activity c, biological activity assay measuring epitope specific T cell activation c, biological activity assay measuring epitope specific T cell helper activity c, biological activity assay measuring epitope specific T cell killing c, biological activity assay measuring epitope specific cytokine production by T cells c, biological activity assay measuring epitope specific cytotoxic T cell degranulation c, biological activity assay measuring epitope specific proliferation of T cells c, in vitro assay measuring T cell epitope specific suppression c

assay measuring the association constant [KA] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001719

A B cell epitope binding constant determination assay that measures the association constant KA.
Source
IEDB
is equivalent to
assay measuring a binding constant of a B cell epitope:antibody complex c and (has_specified_output op some equilibrium association constant (KA) c)
has super-classes
assay measuring a binding constant of a B cell epitope:antibody complex c
has sub-classes
ELISA measuring the association constant [KA] of a B cell epitope:antibody complex c, RIA measuring the association constant [KA] of a B cell epitope:antibody complex c, calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex c, chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex c, quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex c, surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex c

assay measuring the association constant [KA] of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001987

A MHC binding constant determination assay measuring equilibrium association constant (KA).
Source
IEDB
is equivalent to
assay measuring a binding constant of a MHC:ligand complex c and (has_specified_output op some equilibrium association constant (KA) c) and (has_specified_output op some has measurement unit label op value count per molar)
has super-classes
assay measuring a binding constant of a MHC:ligand complex c
has sub-classes
cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection c

assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002100

A T cell epitope binding constant determination assay that measures the association constant KA.
Source
IEDB
has super-classes
assay measuring a binding constant of a T cell epitope:MHC:TCR complex c
has_specified_output op some has measurement unit label op value count per nanomolar

assay measuring the dissociation constant [KD] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001708

A B cell epitope binding constant determination assay that measures the dissociation constant KD.
Source
IEDB
is equivalent to
assay measuring a binding constant of a B cell epitope:antibody complex c and (has_specified_output op some equilibrium dissociation constant (KD) c)
has super-classes
assay measuring a binding constant of a B cell epitope:antibody complex c
has sub-classes
ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 c, bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c

assay measuring the dissociation constant [KD] of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001988

A MHC binding constant determination assay measuring equilibrium dissociation constant (KD).
Source
IEDB
is equivalent to
assay measuring a binding constant of a MHC:ligand complex c and (has_specified_output op some equilibrium dissociation constant (KD) c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring a binding constant of a MHC:ligand complex c
has sub-classes
cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection c, cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection c, cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection c, purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection c, purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection c, purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection c

assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002097

A T cell epitope binding constant determination assay that measures the dissociation constant KD.
Source
IEDB
is equivalent to
assay measuring a binding constant of a T cell epitope:MHC:TCR complex c and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring a binding constant of a T cell epitope:MHC:TCR complex c
has sub-classes
plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex c

assay measuring the half life of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001990

A MHC binding constant determination assay measuring half life of binding.
Source
IEDB
is equivalent to
assay measuring a binding constant of a MHC:ligand complex c and (has_specified_output op some half life of binding datum c)
has super-classes
assay measuring a binding constant of a MHC:ligand complex c
has sub-classes
cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection c, cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection c, cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection c, purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection c

assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001991

A MHC binding constant determination assay measuring half maximal effective concentration (EC50).
Source
IEDB
is equivalent to
assay measuring a binding constant of a MHC:ligand complex c and (has_specified_output op some half maximal effective concentration (EC50) c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring a binding constant of a MHC:ligand complex c
has sub-classes
cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection c, cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection c, purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection c

assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001992

A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50).
Source
IEDB
is equivalent to
assay measuring a binding constant of a MHC:ligand complex c and (has_specified_output op some half maximal inhibitory concentration (IC50) c)
has super-classes
assay measuring a binding constant of a MHC:ligand complex c
has sub-classes
cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition c, cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection c, cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection c, purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection c, purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection c

assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001994

A MHC binding constant determination assay measuring binding on rate (kon).
Source
IEDB
is equivalent to
assay measuring a binding constant of a MHC:ligand complex c and (has_specified_output op some binding on rate measurement datum (kon) c)
has super-classes
assay measuring a binding constant of a MHC:ligand complex c
has sub-classes
cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection c

assay measuring the off rate [koff] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001723

A B cell epitope binding constant determination assay that measures the off rate.
Source
IEDB
is equivalent to
assay measuring a binding constant of a B cell epitope:antibody complex c and (has_specified_output op some binding off rate measurement datum (koff) c)
has super-classes
assay measuring a binding constant of a B cell epitope:antibody complex c
has sub-classes
bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex c, quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex c, surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex c

assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002099

A T cell epitope binding constant determination assay that measures the off rate.
Source
IEDB
has super-classes
assay measuring a binding constant of a T cell epitope:MHC:TCR complex c
has_specified_output op some has measurement unit label op value hertz

assay measuring the off rate measurement [koff] of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001993

A MHC binding constant determination assay measuring binding off rate measurement data item (koff).
Source
IEDB
is equivalent to
assay measuring a binding constant of a MHC:ligand complex c and (has_specified_output op some binding off rate measurement datum (koff) c) and (has_specified_output op some has measurement unit label op value hertz)
has super-classes
assay measuring a binding constant of a MHC:ligand complex c
has sub-classes
cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection c, cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection c, purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection c

assay measuring the on rate [kon] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001718

A B cell epitope binding constant determination assay that measures the on rate.
Source
IEDB
is equivalent to
assay measuring a binding constant of a B cell epitope:antibody complex c and (has_specified_output op some binding on rate measurement datum (kon) c)
has super-classes
assay measuring a binding constant of a B cell epitope:antibody complex c
has sub-classes
bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex c, quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex c, surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex c

assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002098

A T cell epitope binding constant determination assay that measures the on rate.
Source
IEDB
has super-classes
assay measuring a binding constant of a T cell epitope:MHC:TCR complex c
has_specified_output op some has measurement unit label op value count per molar second

assay objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000441

an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
Source
PPPB branch
Example
the objective to determine the weight of a mouse.
has super-classes
objective specification c
has sub-classes
analyte measurement objective c

assay using chromatin immunoprecipitationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001956

an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification
Example
http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html
is equivalent to
(has part op some immunoprecipitation c) and (achieves_planned_objective op some epigenetic modification identification objective c or protein and DNA interaction identification objective c)
has super-classes
immunoprecipitation assay c
has sub-classes
ChIP assay c, ChIP-chip assay c, ChIP-seq assay c, MeDIP-seq assay c, chromatin interaction analysis by paired-end tag sequencing c

assay validation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001160

an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
Source
GROUP: Penn Group
has super-classes
objective specification c

assemblyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001248

A region of the genome of known length that is composed by ordering and aligning two or more different regions.
has super-classes
region c
has sub-classes
sequence_assembly c

assigning a centrally registered identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000574

a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
Example
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
has super-classes
planned process c
has_specified_output op some centrally registered identifier symbol c
has participant op some centrally registered identifier registry c

assigning gene property based on phenotypic assessmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001575

Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result.
Source
Philly workshop 2011
has super-classes
drawing a conclusion based on data c
has_specified_input op some is_specified_output_of op some comparative phenotypic assessment c

associating information with a centrally registered identifier in its registryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000575

A planned process in which a CRID registry associates an information content entity with a CRID symbol
Example
Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
has super-classes
planned process c
has_specified_input op some information content entity c
has_specified_input op some centrally registered identifier symbol c
has participant op some centrally registered identifier registry c

atmospherec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001498

A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
Source
MO_219 atmosphere
has super-classes
growth environment c

atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33250

A chemical entity constituting the smallest component of an element having the chemical properties of the element.
has super-classes
material entity c
has sub-classes
deuterium atom c, phosphorus-32 atom c, phosphorus-33 atom c, rare earth metal atom c

atomic emission detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000642

Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element.
Source
WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086
has super-classes
gas chromatography detector c

author contributions sectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000323

A part of a publication that is about the specific contributions of each author
Example
LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
has super-classes
document part c

author identificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000302

A textual entity intended to identify a particular author
Example
L. Hunter
has super-classes
written name c

author listc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000321

part of a document that enumerates the authors of the document
Example
Lawrence Hunter and Kevin Brettonel Cohen
has super-classes
document part c
has part op some author identification c

author rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000442

A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
has super-classes
role c

auto injectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000610

A gas chromatography device that can auto-inject a small number of samples an inlet.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058
has super-classes
sample injection system c

autoclavec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001112

A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents.
Source
J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave
has super-classes
environmental control device c
has function op some heat function c
has function op some mechanical function c
has function op some sterilization function c

autoimmune diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110054

Is a disease characterized by an immune response of an organism against parts of itself
Source
IEDB
has super-classes
disease c

automatic staining machinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001063

A device that is used to automatically stain tissue sections on slides or tissue specimens.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some mechanical function c
has function op some addition of molecular tracer function c

automatic tissue processorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001064

A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
Source
United States Patent 3762362
has super-classes
device c
has function op some mechanical function c
has function op some reagent application function c

autosamplerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000555

An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. \n alt The autosampler is an automatic sample changer device.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002
has super-classes
device c
has sub-classes
Bruker autosampler c

autotransplantationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000171

is the transplantation of tissue from one part of \nthe body to another in the same individual. )
Source
OBI branch derived
has super-classes
transplantation c

avalanche photodiodec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400011

An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
C30644E - InGaAs Avalanche Photodiode
has super-classes
photodiode c

AVANCE II spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000580

A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently.
Source
WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197
has super-classes
Bruker NMR instrument c

average depth of sequence coveragec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001618

An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
Source
NIAID GSCID-BRC metadata working group
has super-classes
average value c

average linkage hierarchical clusteringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200043

An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster.
Source
PERSON: Elisabetta Manduchi
has super-classes
agglomerative hierarchical clustering c

average valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000679

A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
is equivalent to
is_specified_output_of op some averaging data transformation c
has super-classes
data item c
has sub-classes
average depth of sequence coverage c

averaging data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200170

An averaging data transformation is a data transformation that has objective averaging.
Source
PERSON: James Malone
is equivalent to
(has_specified_output op some average value c) or (achieves_planned_objective op some averaging objective c)
has super-classes
data transformation c
has sub-classes
arithmetic mean calculation c, moving average c

averaging objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000425

An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
Source
PERSON: Elisabetta Manduchi
Example
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
has super-classes
data transformation objective c

B cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000236

A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
has super-classes
lymphocyte c
has sub-classes
plasma cell c

b cell epitope predictionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200058

A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope.
Source
PERSON: Helen Parkinson
has super-classes
sequence analysis data transformation c
achieves_planned_objective op some sequence analysis objective c

B cell epitope specific antibody-dependent cellular cytotoxicityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001717

antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope
Source
IEDB (QTT)
is equivalent to
antibody-dependent cellular cytotoxicity c and (process is result of op some immunoglobulin binding to epitope c)
has super-classes
antibody-dependent cellular cytotoxicity c

B cell epitope specific complement-dependent cytotoxicityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001716

complement-dependent cytotoxicity resulting from antibody binding to epitope
Source
IEDB (QTT)
is equivalent to
complement-dependent cytotoxicity c and (process is result of op some immunoglobulin binding to epitope c)
has super-classes
complement-dependent cytotoxicity c

B cell epitope specific histamine secretion mediated by immunoglobulinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001725

histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope
Source
IEDB (QTT)
is equivalent to
histamine secretion mediated by immunoglobulin c and (process is result of op some immunoglobulin binding to epitope c)
has super-classes
histamine secretion mediated by immunoglobulin c

B cell epitope specific hypersensitivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001722

hypersensitivity resulting from antibody binding to epitope
Source
IEDB (QTT)
is equivalent to
hypersensitivity c and (process is result of op some immunoglobulin binding to epitope c)
has super-classes
hypersensitivity c

B cell epitope specific immune complex formationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001720

immune complex formation resulting from antibody binding to epitope
Source
IEDB (QTT)
is equivalent to
immune complex formation c and immunoglobulin binding to epitope c
has super-classes
immune complex formation c
immunoglobulin binding to epitope c

B cell epitope specific immune interventionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001487

An epitope specific immune intervention in which the induced response targets a B cell epitope
Source
IEDB
Example
Injecting a mouse with recombinant antibody targeting an anthrax epitope
has super-classes
epitope specific immune intervention c

B cell epitope specific immunoglobulin-mediated neutralizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001714

immunoglobulin-mediated neutralization resulting from antibody binding to epitope
Source
IEDB (QTT)
is equivalent to
immunoglobulin-mediated neutralization c and (process is result of op some immunoglobulin binding to epitope c)
has super-classes
immunoglobulin-mediated neutralization c

B cell epitope specific opsonizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001713

opsonization resulting from antibody binding to epitope
Source
IEDB (QTT)
is equivalent to
opsonization c and (process is result of op some immunoglobulin binding to epitope c)
has super-classes
opsonization c

B cell receptor complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0019815

An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
has super-classes
adaptive immune receptor c

B cell tolerance inductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0002514

A process involving any mechanism for tolerance induction in B cells.
has super-classes
tolerance induction c

b transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200109

A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization.
Source
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Example
This type of transformation is typically used in flow cytometry.
has super-classes
normalization data transformation c
(has_specified_output op some normalized data set c) and (achieves_planned_objective op some data normalization objective c)

background corrected data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000660

A data set that is produced as the output of a background correction data transformation.
is equivalent to
is_specified_output_of op some background correction data transformation c
has super-classes
data set c

background corrected data visualizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200193

A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type.
has super-classes
data visualization c
has_specified_output op some density plot c or histogram c
has_specified_input op only background corrected data set c

background correction data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000666

A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
Source
PERSON: James Malone
is equivalent to
(has_specified_output op some background corrected data set c) or (achieves_planned_objective op some background correction objective c)
has super-classes
data transformation c

background correction objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200173

A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
Source
PERSON: Elisabetta Manduchi
has super-classes
correction objective c

Bacteriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2

has super-classes
organism c

bacterial one-hybrid c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001682

is a method for identifying the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence
Source
http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system
Example
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. Nucleic Acids Res. 2008 May;36(8):2547-60. Epub 2008 Mar 10. PMID: 18332042
is equivalent to
(assay c and (has_specified_input op some genetically modified material c) and (has_specified_output op some data item c and (is about op some sequence-specific DNA binding c))) and (achieves_planned_objective op some protein and DNA interaction identification objective c)
has super-classes
yeast one-hybrid c

Bactiflowc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400012

A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes.
Source
http://www.chemunex.com/products/chemframe.htm
has super-classes
flow cytometer analyzer c

balancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001135

A measuring instrument that is used to determine the weight or mass of an object.
Source
http://en.wikipedia.org/wiki/Weighing_scale
has super-classes
measurement device c
has function op some mechanical function c
has function op some measure function c
has sub-classes
analytical balance c, mechanical balance c, top loading balance c

balanced incomplete block designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500008

balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i'
Source
http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html
Example
PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice.
has super-classes
factorial design c

band pass filterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400013

A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others.
Source
http://en.wikipedia.org/wiki/Band_pass_filter
Example
530/30 BP filter, 585/42 BP filter
has super-classes
optical filter c

baseline participant rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000143

a reference participant role which is realized by making the reference to qualities at the start of the study or intervention
Example
Subject at time = 0; subject before a stress test.
has super-classes
reference subject role c

basophilc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000767

Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
has super-classes
cell c

bead array readerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001109

A device that is used to acquire and image bead array data.
Source
PERSON: Erik Segerdell
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

behavioral qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000186

An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
has super-classes
quality of a single physical entity c
has sub-classes
handedness c

Benjamini and Hochberg false discovery rate correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200036

A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
Source
Helen Parkinson
Example
Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)
has super-classes
false discovery rate correction method c
has_specified_input op some p-value c
has_specified_output op some error corrected data set c
has_specified_output op some q-value c
achieves_planned_objective op some multiple testing correction objective c

Benjamini and Yekutieli false discovery rate correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200049

A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
Source
Helen Parkinson
Example
The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)
has super-classes
false discovery rate correction method c
has_specified_input op some p-value c
has_specified_output op some error corrected data set c
has_specified_output op some q-value c
achieves_planned_objective op some multiple testing correction objective c

Berichrom(r) Antithrombin III (A) Kitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000815

For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution
Source
WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06
has super-classes
processed material c

Bernoulli trialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000117

is an assay where the output data is a datum with one of two values denoted success and failure.
Source
OBI branch derived
has super-classes
assay c
achieves_planned_objective op some assay objective c

biexponential transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200006

A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation.
Source
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Example
This type of transformation is typically used in flow cytometry.
has super-classes
curve fitting data transformation c
normalization data transformation c
(has_specified_output op some normalized data set c) and (achieves_planned_objective op some data normalization objective c)
achieves_planned_objective op some curve fitting objective c

Bilateriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_33213

has super-classes
Opisthokonta c
has sub-classes
Ecdysozoa c, Vertebrata <Metazoa> c

bilec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001970

vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
has super-classes
organism substance c

bile specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002501

A specimen that is derived from bile.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some bile c))
has super-classes
specimen from organism c

bindingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001588

The process of material entities forming complexes.
Source
IEDB
Example
A peptide binding to an MHC molecule to form a complex.
has super-classes
biological_process c
has sub-classes
MHC protein complex binding to ligand c, MHC:epitope complex binding to TCR c, core promoter binding c, immunoglobulin binding to epitope c, protein domain specific binding c, sequence-specific DNA binding c

binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001146

An assay with the objective to characterize the disposition of two or more material entities to form a complex.
Source
PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
Example
Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
is equivalent to
assay c and (has_specified_output op some is about op some binding c)
has super-classes
assay c
has sub-classes
3D structure determination of bound complex assay c, MHC ligand assay c, Sos-recruitment assay c, assay measuring qualitiative binding of a B cell epitope:antibody complex c, assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex c, binding constant determination assay c, bio-layer interferometry assay c, calorimetric binding assay c, competitive inhibition of binding assay c, direct binding assay c, electrophoretic mobility shift assay c, far-Western blot c, fluorescence detection binding assay c, phage display binding assay c, promoter activity detection by reporter gene assay c, radioactivity detection binding assay c, split-ubiquitin assay c, surface plasmon resonance binding assay c, transcription factor binding site assay c, yeast 2-hybrid c, yeast one-hybrid c

binding constantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001144

A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process
Example
The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes".
is equivalent to
equilibrium dissociation constant (KD) c or equilibrium association constant (KA) c or equilibrium dissociation constant (KD) approximated by IC50 c or equilibrium dissociation constant (KD) approximated by EC50 c or half life of binding datum c or binding off rate measurement datum (koff) c or binding on rate measurement datum (kon) c
has super-classes
binding datum c
has sub-classes
binding off rate measurement datum (koff) c, binding on rate measurement datum (kon) c, equilibrium association constant (KA) c, equilibrium dissociation constant (KD) c, equilibrium dissociation constant (KD) approximated by EC50 c, equilibrium dissociation constant (KD) approximated by IC50 c, half life of binding datum c

binding constant determination assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001025

A binding assay where the specified output is a binding constant
Example
Determination of KD value for an antibody binding a protein using a BIACORE assay.
is equivalent to
binding assay c and (has_specified_output op some binding constant c)
has super-classes
binding assay c
has sub-classes
assay measuring a binding constant of a B cell epitope:antibody complex c, assay measuring a binding constant of a MHC:ligand complex c, assay measuring a binding constant of a T cell epitope:MHC:TCR complex c

binding datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001181

A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
is equivalent to
data item c and (is about op some binding c)
has super-classes
data item c
has sub-classes
50% dissociation of binding temperature (Tm) c, binding constant c, negative binding datum c

binding off rate measurement datum (koff)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001603

A rate measurement datum of how quickly bound complexes disassociate
Source
IEDB
has super-classes
binding constant c
rate measurement datum c

binding on rate measurement datum (kon)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001605

A rate measurement datum of how quickly bound complexes form
Source
IEDB
has super-classes
binding constant c
rate measurement datum c

bio-layer interferometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002107

A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor.
Source
IEDB
Example
Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds.
has super-classes
binding assay c

bio-layer interferometry assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002104

A B cell epitope qualitative binding to antibody assay that uses a bio-layer interferometry assay.
Source
IEDB
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c
has part op some bio-layer interferometry assay c

bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002105

A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a bio-layer interferometry assay.
Source
IEDB
has super-classes
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c
has part op some bio-layer interferometry assay c
has_specified_output op some has measurement unit label op value nanomolar

bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002103

A B cell epitope assay that measures the off rate using a bio-layer interferometry assay.
Source
IEDB
has super-classes
assay measuring the off rate [koff] of a B cell epitope:antibody complex c
has part op some bio-layer interferometry assay c
has_specified_output op some has measurement unit label op value hertz

bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002102

A B cell epitope assay that measures the on rate using a bio-layer interferometry assay.
Source
IEDB
has super-classes
assay measuring the on rate [kon] of a B cell epitope:antibody complex c
has part op some bio-layer interferometry assay c
has_specified_output op some has measurement unit label op value count per molar second

biodiversity assessment objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001969

biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level
Source
PRS for OBI
has super-classes
biological feature identification objective c

Bioinformatics Resource Centerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001626

An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
Source
Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
has super-classes
organization c

Bioinformatics Resource Center contact personc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001883

A person who is the contact representative of a Bioinformatics Resource Center
Source
NIAID GSCID-BRC metadata working group
is equivalent to
Homo sapiens c and (is member of organization op some Bioinformatics Resource Center c) and (has role op some contact representative role c)
has super-classes
Homo sapiens c

biological activity assay measuring B cell epitope specific in vivo activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001698

A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment.
Source
IEDB
is equivalent to
assay measuring B cell epitope specific biological activity c and (has part op some in vivo intervention experiment c) and (has_specified_input op some organism c)
has super-classes
assay measuring B cell epitope specific biological activity c
has sub-classes
in vivo assay measuring B cell epitope specific disease exacerbation c, in vivo assay measuring B cell epitope specific induction of hypersensitivity c, in vivo assay measuring B cell epitope specific protection from challenge c, in vivo assay measuring B cell epitope specific protection from fertility c, in vivo assay measuring B cell epitope specific tolerance induction c, in vivo assay measuring B cell epitope specific treatment of disease c

biological activity assay measuring epitope specific activation of additional immune response in vitroc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001704

A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity.
Source
IEDB
has super-classes
assay measuring B cell epitope specific biological activity c
has_specified_output op some information content entity c and (is about op some process is result of op some immunoglobulin binding to epitope c)
has sub-classes
biological activity assay measuring epitope specific Ig-mediated histamine release c, biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity c, biological activity assay measuring epitope specific complement-dependent cytotoxicity c, biological activity assay measuring epitope specific immune complex formation c, biological activity assay measuring epitope specific opsonization c

biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001642

A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific activation of additional immune response in vitro c and (has_specified_output op some information content entity c and (is about op some antibody-dependent cellular cytotoxicity c and (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
biological activity assay measuring epitope specific activation of additional immune response in vitro c

biological activity assay measuring epitope specific antigen inhibition of antibody activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001705

A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen.
Source
IEDB
has super-classes
assay measuring B cell epitope specific biological activity c
has_specified_input op some material entity c and (has role op some positive reference substance role c)

biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001276

A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-C motif) ligand 1 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c, ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c, cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c, intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c

biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002056

A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-C motif) ligand 17 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells c

biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001775

A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-C motif) ligand 19 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells c

biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001774

A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-C motif) ligand 21 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells c

biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001777

A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-C motif) ligand 22 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells c

biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001345

A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-C motif) ligand 4 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c, ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c, cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c, intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c

biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001776

A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-X-C motif) ligand 12 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells c

biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001779

A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-X-C motif) ligand 13 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells c

biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001778

A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-X-C motif) ligand 16 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells c

biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001459

A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-X-C motif) ligand 9 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c, ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c, cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c, intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c

biological activity assay measuring epitope specific complement-dependent cytotoxicityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001641

A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific activation of additional immune response in vitro c and (has_specified_output op some information content entity c and (is about op some complement-dependent cytotoxicity c and (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
biological activity assay measuring epitope specific activation of additional immune response in vitro c

biological activity assay measuring epitope specific cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110129

A T cell epitope dependent biological activity assay that detects cytokine production.
Source
IEDB
has super-classes
assay measuring T cell epitope specific biological activity c
has_specified_output op some information content entity c and (is about op some cytokine production c)
has sub-classes
biological activity assay measuring epitope specific IP-10 production by T cells c, biological activity assay measuring epitope specific RANTES production by T cells c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c, biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells c, biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells c, biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells c, biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c, biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c, biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c, biological activity assay measuring epitope specific interferon-beta production by T cells c, biological activity assay measuring epitope specific interferon-gamma production by T cells c, biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c, biological activity assay measuring epitope specific interleukin-1 beta production by T cells c, biological activity assay measuring epitope specific interleukin-10 production by T cells c, biological activity assay measuring epitope specific interleukin-12 production by T cells c, biological activity assay measuring epitope specific interleukin-13 production by T cells c, biological activity assay measuring epitope specific interleukin-15 production by T cells c, biological activity assay measuring epitope specific interleukin-16 production by T cells c, biological activity assay measuring epitope specific interleukin-17 production by T cells c, biological activity assay measuring epitope specific interleukin-18 production by T cells c, biological activity assay measuring epitope specific interleukin-2 production by T cells c, biological activity assay measuring epitope specific interleukin-21 production by T cells c, biological activity assay measuring epitope specific interleukin-22 production by T cells c, biological activity assay measuring epitope specific interleukin-23 production by T cells c, biological activity assay measuring epitope specific interleukin-27 production by T cells c, biological activity assay measuring epitope specific interleukin-3 production by T cells c, biological activity assay measuring epitope specific interleukin-4 production by T cells c, biological activity assay measuring epitope specific interleukin-5 production by T cells c, biological activity assay measuring epitope specific interleukin-6 production by T cells c, biological activity assay measuring epitope specific interleukin-7 production by T cells c, biological activity assay measuring epitope specific interleukin-8 production by T cells c, biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c, biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c, biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells c, biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c, biological activity assay measuring epitope specific oncostatin M production by T cells c, biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c, biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c, biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c, biological activity assay measuring interleukin-9 production by T cells c

biological activity assay measuring epitope specific cytotoxic T cell degranulationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001269

A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation.
Source
IEDB
is equivalent to
assay measuring T cell epitope specific biological activity c and (has_specified_output op some information content entity c and (is about op some cytotoxic T cell degranulation c))
has super-classes
assay measuring T cell epitope specific biological activity c
has sub-classes
biological activity assay measuring epitope specific granulysin release by T cells c, biological activity assay measuring epitope specific granzyme A release by T cells c, biological activity assay measuring epitope specific granzyme B release by T cells c, biological activity assay measuring epitope specific perforin release by T cells c

biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001600

A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some granulocyte colony-stimulating factor production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells c, ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells c, cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells c, intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells c

biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001233

A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some granulocyte macrophage colony-stimulating factor production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells c, ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells c, cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells c, cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells c, intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells c

biological activity assay measuring epitope specific granulysin release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001810

A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytotoxic T cell degranulation c and (has_specified_output op some information content entity c and (is about op some granulysin production c))
has super-classes
biological activity assay measuring epitope specific cytotoxic T cell degranulation c
has sub-classes
ELISA measuring epitope specific granulysin release by T cells c, intracellular material detection assay measuring epitope specific granulysin release by T cells c

biological activity assay measuring epitope specific granzyme A release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001809

A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytotoxic T cell degranulation c and (has_specified_output op some information content entity c and (is about op some granzyme A production c))
has super-classes
biological activity assay measuring epitope specific cytotoxic T cell degranulation c
has sub-classes
cytometric bead array assay measuring epitope specific granzyme A release by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells c, intracellular material detection assay measuring epitope specific granzyme A release by T cells c

biological activity assay measuring epitope specific granzyme B release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001436

A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytotoxic T cell degranulation c and (has_specified_output op some information content entity c and (is about op some granzyme B production c))
has super-classes
biological activity assay measuring epitope specific cytotoxic T cell degranulation c
has sub-classes
ELISA measuring epitope specific granzyme B release by T cells c, ELISPOT assay measuring epitope specific granzyme B release by T cells c, cytometric bead array assay measuring epitope specific granzyme B release by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells c, intracellular material detection measuring epitope specific granzyme B release by T cells c

biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001228

A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response.
Source
IEDB
has super-classes
biological activity assay measuring epitope specific T cell helper activity c

biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001263

A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific T cell helper activity c and (has_specified_output op some information content entity c and (is about op some helper T cell enhancement of T cell mediated immune response c)) and (has_specified_output op some information content entity c and (is about op some helper T cell enhancement of T cell mediated immune response c and (process is result of op some MHC:epitope complex binding to TCR c)))
has super-classes
biological activity assay measuring epitope specific T cell helper activity c

biological activity assay measuring epitope specific hemagglutination inhibitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001724

A B cell epitope qualitative binding to antibody assay that uses a viral hemagglutination inhibition assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some viral hemagglutination inhibition assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

biological activity assay measuring epitope specific Ig-mediated histamine releasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001639

A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific activation of additional immune response in vitro c and (has_specified_output op some information content entity c and (is about op some histamine secretion mediated by immunoglobulin c and (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
biological activity assay measuring epitope specific activation of additional immune response in vitro c

biological activity assay measuring epitope specific immune complex formationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001695

A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific activation of additional immune response in vitro c and (has_specified_output op some information content entity c and (is about op some immune complex formation c and (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
biological activity assay measuring epitope specific activation of additional immune response in vitro c

biological activity assay measuring epitope specific immunoglobulin-mediated antigen activationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001640

A B cell epitope dependent biological activity determination assay that detects antigen activation.
Source
IEDB
has super-classes
assay measuring B cell epitope specific biological activity c
has_specified_output op some information content entity c and (is about op some immunoglobulin mediated immune response c and (process is result of op some immunoglobulin binding to epitope c))

biological activity assay measuring epitope specific immunoglobulin-mediated neutralizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001643

A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen.
Source
IEDB
is equivalent to
assay measuring B cell epitope specific biological activity c and (has_specified_output op some information content entity c and (is about op some immunoglobulin-mediated neutralization c and (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
assay measuring B cell epitope specific biological activity c

biological activity assay measuring epitope specific interferon-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001390

A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interferon-beta production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interferon-beta production by T cells c, ELISPOT assay measuring epitope specific interferon-beta production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells c, intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells c

biological activity assay measuring epitope specific interferon-gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001414

A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interferon-gamma production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interferon-gamma production by T cells c, ELISPOT assay measuring epitope specific interferon-gamma production by T cells c, cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells c, cytometric bead array assay measuring epitope specific interferon-gamma production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells c, intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells c, radio immuno assay measuring epitope specific interferon-gamma production by T cells c

biological activity assay measuring epitope specific interleukin-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001388

A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-1 alpha production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-1 alpha production by T cells c, ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells c, cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells c

biological activity assay measuring epitope specific interleukin-1 beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001449

A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-1 beta production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-1 beta production by T cells c, ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells c, cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells c

biological activity assay measuring epitope specific interleukin-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001209

A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-10 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-10 production by T cells c, ELISPOT assay measuring epitope specific interleukin-10 production by T cells c, cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-10 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells c

biological activity assay measuring epitope specific interleukin-12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001391

A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-12 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-12 production by T cells c, ELISPOT assay measuring epitope specific interleukin-12 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-12 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells c

biological activity assay measuring epitope specific interleukin-13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001251

A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-13 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-13 production by T cells c, ELISPOT assay measuring epitope specific interleukin-13 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-13 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells c

biological activity assay measuring epitope specific interleukin-15 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001292

A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-15 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-15 production by T cells c, ELISPOT assay measuring epitope specific interleukin-15 production by T cells c, detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells c

biological activity assay measuring epitope specific interleukin-16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001280

A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-16 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-16 production by T cells c, ELISPOT assay measuring epitope specific interleukin-16 production by T cells c, cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells c

biological activity assay measuring epitope specific interleukin-17 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001295

A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-17 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-17 production by T cells c, ELISPOT assay measuring epitope specific interleukin-17 production by T cells c, biological activity assay measuring epitope specific interleukin-17A production by T cells c, biological activity assay measuring epitope specific interleukin-17F production by T cells c, cytometric bead array assay measuring epitope specific interleukin-17 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells c

biological activity assay measuring epitope specific interleukin-17A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001773

An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17 production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-17A production c))
has super-classes
biological activity assay measuring epitope specific interleukin-17 production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-17A production by T cells c, ELISPOT assay measuring epitope specific interleukin-17A production by T cells c, cytometric bead array assay measuring epitope specific interleukin-17A production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells c

biological activity assay measuring epitope specific interleukin-17F production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001772

An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17 production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-17F production c))
has super-classes
biological activity assay measuring epitope specific interleukin-17 production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-17F production by T cells c, ELISPOT assay measuring epitope specific interleukin-17F production by T cells c, cytometric bead array assay measuring epitope specific interleukin-17F production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells c

biological activity assay measuring epitope specific interleukin-18 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001380

A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-18 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-18 production by T cells c, ELISPOT assay measuring epitope specific interleukin-18 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-18 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells c

biological activity assay measuring epitope specific interleukin-2 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001445

A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells.
Source
IEDB
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has_specified_output op some information content entity c and (is about op some interleukin-2 production c)
has sub-classes
ELISA measuring epitope specific interleukin-2 production by T cells c, ELISPOT assay measuring epitope specific interleukin-2 production by T cells c, cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-2 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells c, promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells c

biological activity assay measuring epitope specific interleukin-21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001237

A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-21 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-21 production by T cells c, ELISPOT assay measuring epitope specific interleukin-21 production by T cells c, cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells c

biological activity assay measuring epitope specific interleukin-22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001217

A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-22 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-22 production by T cells c, ELISPOT assay measuring epitope specific interleukin-22 production by T cells c, cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells c

biological activity assay measuring epitope specific interleukin-23 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001363

A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-23 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-23 production by T cells c, ELISPOT assay measuring epitope specific interleukin-23 production by T cells c, cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells c

biological activity assay measuring epitope specific interleukin-27 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001198

A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-27 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-27 production by T cells c, ELISPOT assay measuring epitope specific interleukin-27 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-27 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells c

biological activity assay measuring epitope specific interleukin-3 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001406

A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-3 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-3 production by T cells c, ELISPOT assay measuring epitope specific interleukin-3 production by T cells c, cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-3 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells c

biological activity assay measuring epitope specific interleukin-4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001450

A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-4 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-4 production by T cells c, ELISPOT assay measuring epitope specific interleukin-4 production by T cells c, cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-4 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells c

biological activity assay measuring epitope specific interleukin-5 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001230

A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-5 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-5 production by T cells c, ELISPOT assay measuring epitope specific interleukin-5 production by T cells c, cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-5 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells c

biological activity assay measuring epitope specific interleukin-6 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001451

A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-6 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-6 production by T cells c, ELISPOT assay measuring epitope specific interleukin-6 production by T cells c, cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-6 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells c

biological activity assay measuring epitope specific interleukin-7 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001587

A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-7 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-7 production by T cells c, ELISPOT assay measuring epitope specific interleukin-7 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-7 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells c

biological activity assay measuring epitope specific interleukin-8 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001218

A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-8 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-8 production by T cells c, ELISPOT assay measuring epitope specific interleukin-8 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-8 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells c

biological activity assay measuring epitope specific IP-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001308

A T cell epitope specific cytokine production assay that detects IP-10 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some IP-10 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific IP-10 production by T cells c, ELISPOT assay measuring epitope specific IP-10 production by T cells c, cytometric bead array assay measuring epitope specific IP-10 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells c, intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells c

biological activity assay measuring epitope specific lymphotoxin A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001327

A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some lymphotoxin A production c))
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific lymphotoxin A production by T cells c, ELISPOT assay measuring epitope specific lymphotoxin A production by T cells c, cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells c, intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells c

biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001333

A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some macrophage inflammatory protein-1 alpha production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c, ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c, cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c, intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c

biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001456

A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some macrophage inflammatory protein-1 gamma production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c, ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c, cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c, intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c

biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002057

A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some macrophage migration inhibitory factor production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells c

biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001465

A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some monocyte chemotactic protein-1 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells c, ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c, cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c, intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c

biological activity assay measuring epitope specific oncostatin M production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002058

A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some Oncostatin M production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
cytometric bead array assay measuring epitope specific oncostatin M production by T cells c

biological activity assay measuring epitope specific opsonizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001644

A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific activation of additional immune response in vitro c and (has_specified_output op some information content entity c and (is about op some opsonization c and (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
biological activity assay measuring epitope specific activation of additional immune response in vitro c

biological activity assay measuring epitope specific perforin release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001497

A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytotoxic T cell degranulation c and (has_specified_output op some information content entity c and (is about op some perforin production c))
has super-classes
biological activity assay measuring epitope specific cytotoxic T cell degranulation c
has sub-classes
ELISPOT assay measuring epitope specific perforin release by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release c, intracellular material detection assay measuring epitope specific perforin release c

biological activity assay measuring epitope specific proliferation of T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110131

A T cell epitope dependent biological activity assay that detects T cell proliferation.
Source
IEDB
is equivalent to
assay measuring T cell epitope specific biological activity c and (has part op some cell proliferation assay c) and (has_specified_output op some information content entity c and (is about op some T cell proliferation c))
has super-classes
assay measuring T cell epitope specific biological activity c
has sub-classes
in vitro assay measuring epitope specific proliferation of T cells c, in vivo assay measuring epitope specific proliferation of T cells c

biological activity assay measuring epitope specific RANTES production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001232

A T cell epitope specific cytokine production assay that detects RANTES production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some chemokine (C-C motif) ligand 5 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific RANTES production by T cells c, ELISPOT assay measuring epitope specific RANTES production by T cells c, cytometric bead array assay measuring epitope specific RANTES production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells c, intracellular cytokine staining assay measuring epitope specific RANTES production by T cells c

biological activity assay measuring epitope specific T cell activationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001407

A T cell epitope dependent biological activity assay that detects T cell activation.
Source
IEDB
has super-classes
assay measuring T cell epitope specific biological activity c

biological activity assay measuring epitope specific T cell helper activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001495

A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function.
Source
IEDB
is equivalent to
assay measuring T cell epitope specific biological activity c and (has_specified_output op some information content entity c and (is about op some helper T cell enhancement of adaptive immune response c)) and (has_specified_output op some information content entity c and (is about op some (helper T cell enhancement of T cell mediated immune response c or helper T cell enhancement of B cell mediated immune response c) and (process is result of op some MHC:epitope complex binding to TCR c)))
has super-classes
assay measuring T cell epitope specific biological activity c
has sub-classes
biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response c, biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response c

biological activity assay measuring epitope specific T cell killingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110130

A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC.
Source
IEDB
is equivalent to
assay measuring T cell epitope specific biological activity c and (has part op some cell-cell killing assay c) and (has_specified_output op some information content entity c and (is about op some T cell mediated cytotoxicity c))
has super-classes
assay measuring T cell epitope specific biological activity c
has sub-classes
in vitro assay measuring epitope specific T cell killing c, in vivo assay measuring epitope specific T cell killing c

biological activity assay measuring epitope specific transforming growth factor-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001264

A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some transforming growth factor beta production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific transforming growth factor-beta production by T cells c, ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells c, cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells c, cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells c, intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells c

biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001607

An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some tumor necrosis factor (ligand) superfamily member 11 production c))
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
has sub-classes
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells c

biological activity assay measuring epitope specific tumor necrosis factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001416

An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some tumor necrosis factor production c))
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific tumor necrosis factor production by T cells c, ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells c, cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells c, cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells c, intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells c

biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001400

A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some tumor necrosis factor superfamily cytokine production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c, ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c, biological activity assay measuring epitope specific lymphotoxin A production by T cells c, biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells c, biological activity assay measuring epitope specific tumor necrosis factor production by T cells c, cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c, intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c

biological activity assay measuring epitope specific vascular endothelial growth factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001570

A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some vascular endothelial growth factor production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific vascular endothelial growth factor production by T cells c, ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells c, cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells c, intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells c

biological activity assay measuring interleukin-9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001253

A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific cytokine production by T cells c and (has_specified_output op some information content entity c and (is about op some interleukin-9 production c))
has super-classes
biological activity assay measuring epitope specific cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-9 production by T cells c, ELISPOT assay measuring epitope specific interleukin-9 production by T cells c, cytometric bead array assay measuring epitope specific interleukin-9 production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells c

biological activity assay measuring T cell epitope specific in vivo activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001484

A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment.
Source
IEDB
is equivalent to
assay measuring T cell epitope specific biological activity c and (has part op some in vivo intervention experiment c) and (has_specified_input op some organism c)
has super-classes
assay measuring T cell epitope specific biological activity c
has sub-classes
in vivo assay measuring T cell epitope specific disease exacerbation c, in vivo assay measuring T cell epitope specific protection from challenge c, in vivo assay measuring T cell epitope specific tolerance induction c, in vivo assay measuring T cell epitope specific treatment of disease c, in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity c

biological feature identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000015

Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
has super-classes
objective specification c
has sub-classes
biodiversity assessment objective c, cellular feature identification objective c, cellular structure feature identification objective c, molecular feature identification objective c, molecular function identification objective c, organism feature identification objective c, organism identification objective c, sequence feature identification objective c

biological replicate rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000198

a reference participant role realized by equivalent treatment of participants
Source
OBI
Example
A member of a dose-time group; a patient in a given arm of a trial
has super-classes
reference subject role c
has sub-classes
cohort role c

biological sexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000047

An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
has super-classes
organismal quality c
has sub-classes
F mating type c, F minus mating type c, a mating type (yeast) c, alpha mating type (yeast) c, female c, h minus c, h plus c, hermaphrodite c, male c

biological vector rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000109

a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
Source
OBI and Wikipedia
Example
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
has super-classes
Obsolete Class c

biological_processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0008150

Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
has super-classes
process c
has sub-classes
DNA methylation c, DNA replication c, T cell activation c, actin filament polymerization c, actin polymerization-dependent cell motility c, antibody-dependent cellular cytotoxicity c, antigen processing and presentation c, binding c, blood coagulation c, cell cycle c, cell killing c, cell proliferation c, cellular developmental process c, cellular process c, chromosome organization c, cytokine production c, disease course c, disease stage c, environmental exposure to infectious agent c, environmental proximity to infectious agent c, epitope binding by adaptive immune receptor c, exposure resulting in immune reactivity c, fertilization c, gene expression c, glucose metabolic process c, granulysin production c, granzyme A production c, granzyme B production c, hemopoiesis c, histone modification c, host exposure to infectious agent c, hypersensitivity c, immunization c, immunoglobulin mediated histamine release c, immunoglobulin mediated immune response c, life cycle stage c, macromolecule localization c, pathologic process c, perforin production c, phagocytosis c, regulation of molecular function, epigenetic c, response to stimulus c, tolerance induction c
is disjoint with
planned process c

biomaterial purityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001339

A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial.
has super-classes
quality of a single physical entity c

bioreactorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001046

A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT
Source
http://en.wikipedia.org/wiki/Bioreactor
has super-classes
physical store c
has function op some mechanical function c
has function op some environment control function c

BioSorter1000c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400014

A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter.
Source
http://www.unionbio.com/products/BioSorter.html
Example
BioSorter 1000 at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

BioSorter2000c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400015

A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter.
Source
http://www.unionbio.com/products/BioSorter.html
Example
BioSorter 2000 at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

BioSorter250c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400016

A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter.
Source
http://www.unionbio.com/products/BioSorter.html
Example
BioSorter 250 at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

BioSorter500c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400017

A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length.
Source
http://www.unionbio.com/products/BioSorter.html
Example
BioSorter 500 at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

biotinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_15956

An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.
has super-classes
molecular label c
has role op some molecular label role c

bisulfite sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000748

An assay which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
Source
adapted from Wikipedia
Example
PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Genome Res. 2009 Jul 6.
has super-classes
DNA sequencing c
DNA methylation profiling by high throughput sequencing assay c
has part op some DNA sequencing c
realizes op some reagent role c and (inheres in op some hydrogensulfite c)
has_specified_input op some deoxyribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some measurement datum c and (is about op some DNA residue methylation c)
has_specified_output op some DNA sequence data c and (is about op some regulation of DNA methylation c)
achieves_planned_objective op some epigenetic modification identification objective c
has participant op some DNA sequencer c
has sub-classes
MethylC-Capture sequencing assay c, Tet-assisted bisulfite sequencing assay c, reduced representation bisulfite sequencing assay c, shotgun bisulfite-seq assay c

bloodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000178

A fluid that is composed of blood plasma and erythrocytes.
has super-classes
organism substance c

blood coagulationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0007596

The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
has super-classes
biological_process c

blood harvestingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110095

A material separation where blood is taken from an organism.
Source
IEDB
has super-classes
material component separation c
has_specified_output op some blood specimen c

blood plasma specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100016

a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
Source
WEB: http://en.wikipedia.org/wiki/Blood_plasma
Example
PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
has super-classes
processed specimen c
material entity c and (has role op some specimen role c)
is_specified_output_of op some material component separation c and (has_specified_input op some blood specimen c)

blood serum specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100017

A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
Source
WEB: http://en.wikipedia.org/wiki/Blood_plasma
Example
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
has super-classes
processed specimen c
is_specified_output_of op some (filtration c or centrifugation c or dialysis c) and (has_specified_input op some blood specimen c)
has role op some specimen role c

blood specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000655

a material entity derived from a portion of blood collected from an organism
Source
Bjoern Peters
Example
blood drawn from a human for glucose assay
has super-classes
specimen from organism c
is_specified_output_of op some collecting specimen from organism c
has role op some specimen role c
derives from op some blood c

blot modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000394

A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
Source
sep:00092
has super-classes
device c
has function op some transfer function c

bone marrowc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002371

the soft tissue that fills the cavities of bones
has super-classes
tissue c

bone marrow specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002512

A specimen that is derived from bone marrow.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some bone marrow c))
has super-classes
specimen from organism c

boostrappingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200035

Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient
Source
Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points
Example
Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved.
has super-classes
statistical model validation c
achieves_planned_objective op some cross validation objective c

box-cox transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200007

A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
Source
ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

brainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000955

The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
has super-classes
material anatomical entity c

brain specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002516

A specimen that is derived from brain.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some brain c))
has super-classes
specimen from organism c

BrdU assay measuring epitope specific proliferation of T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110181

A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay.
Source
IEDB
is equivalent to
in vitro assay measuring epitope specific proliferation of T cells c and (has part op some BrdU incorporation assay c)
has super-classes
in vitro assay measuring epitope specific proliferation of T cells c

BrdU incorporation assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000664

A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies.
Source
IEDB
Example
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU.
has super-classes
cell proliferation assay c
(realizes op some molecular label role c and (inheres in op some 5-bromo-2'-deoxyuridine c)) and (has_specified_input op some 5-bromo-2'-deoxyuridine c)

breastc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000310

The upper ventral region of an animal's torso.
has super-classes
material anatomical entity c

breast specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002523

A specimen that is derived from breast.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some breast c))
has super-classes
specimen from organism c

bromophenol bluec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_59424

3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.
has super-classes
molecular entity c

bromouridine labeling and sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002113

An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs.
Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009065/
has super-classes
RNA-seq assay c

bromouridine pulse-chase and sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002114

An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time.
Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009065/
has super-classes
RNA-seq assay c

bronchial alveolar lavagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100067

Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
Source
GROUP: IEDB
Example
solution containing lung derived T cells, eosinophils, and TNFa.
has super-classes
specimen c
has role op some specimen role c
is_specified_output_of op only lavage c

Bruker 1mm MicroProbec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000590

Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:\n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)\n excellent solvent suppression properties\n virtually no salt effect\n discrete samples in tubes that can be sealed and stored\n automation accessory for sample preparation and handling available.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194
has super-classes
Bruker NMR probe c

Bruker AC series NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000541

A series of older Bruker NMR magnets, now out of production.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241
has super-classes
Bruker NMR instrument c

Bruker AMX series NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000514

A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe.
Source
WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240
has super-classes
Bruker NMR instrument c

Bruker AutoClean systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000475

NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material.
Source
WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205
has super-classes
NMR tube washing system c

Bruker autosamplerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000464

A Bruker autosampler is an autosampler made by Bruker.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209
has super-classes
autosampler c
has sub-classes
Bruker B-ACS system c, Bruker BEST NMR system c, Bruker NMR Case sample changer c, Bruker SampleJet system c

Bruker B-ACS systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000492

The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit.
Source
WEB:<http://www.bruker-biospin.com/automation.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210
has super-classes
Bruker autosampler c

Bruker BEST NMR systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000591

The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data.
Source
WEB:<http://www.bruker-biospin.com/automation.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206
has super-classes
Bruker autosampler c

Bruker Capillary LC-NMR platformc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000553

Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process.
Source
WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279
has super-classes
Bruker NMR instrument c

Bruker CryoProbec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000531

The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:\n Significant S/N gains (with moderately salty samples also)\n Short pulse widths\n Short ring down times\n Linear behavior in power response\n Gradient capability\n CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher\n All high resolution probes have a lock circuit\n All high resolution probes have Z-gradient.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191
has super-classes
Bruker NMR probe c

Bruker high resolution probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000480

BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223
has super-classes
Bruker NMR probe c
has sub-classes
flow high resolution probe c, high resolution magic angle spin probe c, high resolution probe with automatic tuning and matching c

Bruker LC-NMR platformc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000503

The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup.
Source
WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276
has super-classes
Bruker NMR instrument c

Bruker LC-NMR/MS platformc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000582

Includes the connection to a high-resolution TOF-LC-MS system.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277
has super-classes
Bruker NMR instrument c

Bruker MATCH tube holder systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000612

The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.\n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211
has super-classes
NMR sample holder c

Bruker Metabolic Profilerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000632

An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis.
Source
WEB:<http://www.bruker-biospin.com/metabolicprofiler.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199
has super-classes
Bruker NMR instrument c

Bruker micro imaging probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000620

For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples.
Source
WEB:<http://www.bruker-biospin.com/probes_microimaging.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225
has super-classes
Bruker NMR probe c

Bruker NMR Case sample changerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000473

The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats.
Source
WEB:<http://www.bruker-biospin.com/automation.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203
has super-classes
Bruker autosampler c

Bruker NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000596

An NMR instrument that is manufactured by Bruker.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198
has super-classes
NMR instrument c
has sub-classes
AVANCE II spectrometer c, Bruker AC series NMR instrument c, Bruker AMX series NMR instrument c, Bruker Capillary LC-NMR platform c, Bruker LC-NMR platform c, Bruker LC-NMR/MS platform c, Bruker Metabolic Profiler c, Bruker SPE-NMR platform c

Bruker NMR magnetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000597

An NMR magnet that is manufactured by Bruker.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186
has super-classes
NMR magnet c
has sub-classes
Bruker US 2 NMR magnet c, Bruker UltraShield NMR magnet c, Bruker UltraShield Plus NMR magnet c, Bruker Ultrastabilized NMR magnet c

Bruker NMR probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000561

An NMR probe that is manufactured by Bruker.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231
has super-classes
NMR probe c
has sub-classes
Bruker 1mm MicroProbe c, Bruker CryoProbe c, Bruker high resolution probe c, Bruker micro imaging probe c, Bruker solid magic angle spinning probe c

Bruker SampleJet systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000624

Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.\n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement.
Source
WEB:<http://www.bruker-biospin.com/automation.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208
has super-classes
Bruker autosampler c

Bruker SampleRail systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000544

This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back.
Source
WEB:<http://www.bruker-biospin.com/automation.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207
has super-classes
device c
has function op some transfer function c

Bruker solid magic angle spinning probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000629

Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193
has super-classes
Bruker NMR probe c

Bruker SPE-NMR platformc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000613

A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278
has super-classes
Bruker NMR instrument c

Bruker UltraShield NMR magnetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000567

An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design.
Source
WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187
has super-classes
Bruker NMR magnet c

Bruker UltraShield Plus NMR magnetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000530

An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications.
Source
WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190
has super-classes
Bruker NMR magnet c

Bruker Ultrastabilized NMR magnetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000575

An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized.
Source
WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188
has super-classes
Bruker NMR magnet c

Bruker US 2 NMR magnetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000467

An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion.
Source
WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189
has super-classes
Bruker NMR magnet c

buffer rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302731

a role which inheres in some molecular entity realized during the process of buffering
Source
OBI
Example
A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution
has super-classes
role c

C1R cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110029

A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)).
Source
IEDB
has super-classes
immortal cell line c

Caenorhabditis elegansc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_6239

has super-classes
Ecdysozoa c

calibrationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000818

A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements.
Source
WEB:http://en.wikipedia.org/wiki/calibration
Example
the process of using pH buffer adjust a pH meter
has super-classes
planned process c
has part op some assay c
has_specified_output op some measurement device c

calibration substance rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000129

A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance
Example
pH buffer used to calibrate a pH meter bears a calibration substance role
has super-classes
reference substance role c
realized in op only calibration c

calorimeterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000930

A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
Source
http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm
has super-classes
measurement device c
has function op some measure function c

calorimetric binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001634

A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy.
Source
IEDB
Example
A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (ΔH) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell .
is equivalent to
binding assay c and ((realizes op some function c and (inheres in op some calorimeter c)) and (has_specified_input op some calorimeter c))
has super-classes
binding assay c

calorimetry assay measuring binding of a B cell epitope:antibody complex c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001645

A B cell epitope qualitative binding to antibody assay that uses a calorimetric binding assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some calorimetric binding assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001733

A B cell epitope equilibrium association constant (KA) determination assay that uses a calorimetric binding assay.
Source
IEDB
is equivalent to
assay measuring the association constant [KA] of a B cell epitope:antibody complex c and (has part op some calorimetric binding assay c) and (has_specified_output op some has measurement unit label op value count per nanomolar)
has super-classes
assay measuring the association constant [KA] of a B cell epitope:antibody complex c

calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001734

A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a calorimetric binding assay.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c and (has part op some calorimetric binding assay c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c

cancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110053

A disease characterized by abnormal and uncontrolled cell division
Source
IEDB
has super-classes
disease c

cancer cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001906

An immortal cell line derived from a transformed cell that was part of a malignant tumor.
has super-classes
immortal cell line c
is_specified_output_of op some establishing cancer cell line c

canonical variate analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200100

canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form.
Source
WEB: http://en.wikipedia.org/wiki/Canonical_analysis
has super-classes
discriminant analysis c
partitioning data transformation c
achieves_planned_objective op some partitioning objective c

cap analysis of gene expression c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001674

An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome
Source
PMID:14663149
Example
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160
has super-classes
transcription profiling assay c
sequencing assay c
has part op some reverse transcribed polymerase chain reaction c
has part op some DNA sequencing c
has_specified_input op some RNA extract c
has_specified_output op some sequence data c and (is about op some gene expression c)
achieves_planned_objective op some transcription profiling identification objective c
has participant op some DNA sequencer c

capillary blotterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001045

A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed.
Source
http://www.biometra.de/
has super-classes
device c
has function op some transfer function c

capillary columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000496

A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066
has super-classes
chromatography column c

capillary electrophoresis instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001132

An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
Source
http://en.wikipedia.org/wiki/Capillary_electrophoresis
has super-classes
electrophoresis system c

capillary pump systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000546

A pump system optimized for capillary chromatography.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051
has super-classes
chromatography pump system c

capsule shellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000798

a small rounded gelatinous container
Source
http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n
has super-classes
material entity c

captionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000304

A textual entity that describes a figure
Example
Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
has super-classes
textual entity c
is about op some figure c

carbon nanotube columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000628

Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well.
Source
WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107
has super-classes
chromatography column c

Carbon-copy chromosome conformation capture assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001919

An assay that is used to analyze the organization of chromosomes at the genome-wide scale.
Source
"Dostie et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 October; 16(10):1299-309.[PMID:16954542]"
Example
van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094]
has super-classes
sequencing assay c
has part op some DNA sequencing c
has part op some library preparation c
has part op some cross linking c
has part op some multiplex ligation-mediated amplification c
has part op some specific enzymatic cleavage c
realizes op some evaluant role c and (role of op some deoxyribonucleic acid c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some chromosome conformation identification objective c
has participant op some DNA sequencer c
has sub-classes
carbon-copy chromosome conformation capture assay followed by sequencing assay c

carbon-copy chromosome conformation capture assay followed by sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002042

A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture.
Source
Lieberman-Aiden E, et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
Example
Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049.
has super-classes
Carbon-copy chromosome conformation capture assay c

carboxyfluorescein succinimidyl ester staining assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002106

a detection of molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection.
Source
IEDB
Example
Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division.
has super-classes
detection of molecular label c
has part op some fluorescence detection assay c

carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002096

A T cell epitope specific proliferation assay performed on cells in vitro that uses a CFSE assay.
Source
IEDB
is equivalent to
in vitro assay measuring epitope specific proliferation of T cells c and (has part op some carboxyfluorescein succinimidyl ester staining assay c)
has super-classes
in vitro assay measuring epitope specific proliferation of T cells c

CARTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000749

A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
Source
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
has super-classes
decision tree building data transformation c
achieves_planned_objective op some decision tree induction objective c
has members
GenePattern CART ni

cartesian spatial coordinate datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000400

A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
has super-classes
data item c
denotes op some zero-dimensional spatial region c
has coordinate unit label op exactly 1
has sub-classes
one dimensional cartesian spatial coordinate datum c, three dimensional cartesian spatial coordinate datum c, two dimensional cartesian spatial coordinate datum c
is in domain of
has coordinate unit label op, has x coordinate value dp, has y coordinate value dp, has z coordinate value dp

catalytic activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0003824

Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
has super-classes
molecular_function c
has sub-classes
DNA polymerase activity c, RNA-directed DNA polymerase activity c

categorical labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000963

A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
Source
Bjoern Peters
Example
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
has super-classes
datum label c
is in range of
has category label op
has members
ambidexterous ni, left handed ni, right handed ni

categorical measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000938

A measurement datum that is reported on a categorical scale
Source
Bjoern Peters
has super-classes
measurement datum c
has value specification op some categorical value specification c
has sub-classes
handedness categorical measurement datum c
is in domain of
has category label op

categorical value specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001930

A value specification that is specifies one category out of a fixed number of nominal categories
has super-classes
value specification c

cation exchange columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000490

A cation exchange column is a chromatography column that is used in cation exchange chromatography.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096
has super-classes
ion exchange column c

cation trap columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000593

A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278
has super-classes
trap column c

caudate nucleusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001873

Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species.
has super-classes
anatomical cluster c

CD3 subunit with immunoglobulin domainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000001018

A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
has super-classes
protein c

CD4 moleculec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000001004

A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
has super-classes
protein c

CD4-positive, alpha-beta T cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000624

A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
has super-classes
alpha-beta T cell c

CD8 receptorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110132

A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor.
Source
WEB: http://en.wikipedia.org/wiki/CD8
has super-classes
protein c

CD8-positive, alpha-beta cytotoxic T cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000794

A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
has super-classes
CD8-positive, alpha-beta T cell c

CD8-positive, alpha-beta T cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000625

A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
has super-classes
alpha-beta T cell c
has sub-classes
CD8-positive, alpha-beta cytotoxic T cell c

cDNA libraryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000164

Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
Source
GROUP: PSI
Example
PMID:6110205. collection of cDNA derived from mouse splenocytes.
has super-classes
recombinant vector c
is_specified_output_of op some recombinant vector cloning c
has grain op some recombinant vector c

cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000000

A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
Example
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
has super-classes
material entity c
has sub-classes
basophil c, dendritic cell c, epithelial cell c, erythrocyte c, experimentally modified cell in vitro c, fibroblast c, macrophage c, mast cell c, mononuclear cell c, native cell c

cell bound MHC binding assay measuring binding of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001550

A MHC binding qualitative binding to ligand assay measuring MHC ligand binding using MHC present on cells.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a MHC:ligand complex c and (has_specified_input op some cell c and (has part op some MHC protein complex c))
has super-classes
assay measuring qualitiative binding of a MHC:ligand complex c
has sub-classes
cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition c, cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection c, cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection c, cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection c, cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection c

cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001539

A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
fluorescence detection binding assay c
assay measuring the dissociation constant [KD] of a MHC:ligand complex c

cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001549

A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
radioactivity detection binding assay c
assay measuring the dissociation constant [KD] of a MHC:ligand complex c

cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001520

A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
fluorescence detection binding assay c
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c

cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001517

A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
radioactivity detection binding assay c
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c

cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001597

A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding.
Source
IEDB
is equivalent to
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c and (has part op some assay measuring binding of a T cell epitope:MHC:TCR complex c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c

cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001594

A cell bound MHC binding assay that uses fluorescence to detect loss of binding of a known reference ligand due to competition by the ligand under investigation
Source
IEDB
has super-classes
fluorescence detection binding assay c
cell bound MHC binding assay measuring binding of a MHC:ligand complex c
has part op some fluorescence detection assay c
has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)
has_specified_input op some cell c and (has part op some MHC protein complex c)

cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001599

A cell bound MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
has super-classes
radioactivity detection binding assay c
cell bound MHC binding assay measuring binding of a MHC:ligand complex c
has part op some radioactivity detection c
has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)
has_specified_input op some cell c and (has part op some MHC protein complex c)

cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001493

A cell bound MHC binding assay that uses a T cell epitope recognition assay.
Source
IEDB
has super-classes
cell bound MHC binding assay measuring binding of a MHC:ligand complex c
has part op some assay measuring binding of a T cell epitope:MHC:TCR complex c
has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)
has_specified_input op some cell c and (has part op some MHC protein complex c)

cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001666

A cell bound MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value count per nanomolar second)
has super-classes
fluorescence detection binding assay c
assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex c

cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001524

A cell bound MHC ligand binding equilibrium association constant (KA) determination assay that uses fluorescence detection to detect direct binding.
Source
IEDB
is equivalent to
assay measuring the association constant [KA] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value count per molar)
has super-classes
fluorescence detection binding assay c
assay measuring the association constant [KA] of a MHC:ligand complex c

cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001559

A cell bound MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the half life of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value minute)
has super-classes
fluorescence detection binding assay c
assay measuring the half life of a MHC:ligand complex c

cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001558

A cell bound MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the half life of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value minute)
has super-classes
radioactivity detection binding assay c
assay measuring the half life of a MHC:ligand complex c

cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001561

A cell bound MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
fluorescence detection binding assay c
assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex c

cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001665

A cell bound MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the off rate measurement [koff] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some cell c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value hertz)
has super-classes
fluorescence detection binding assay c
assay measuring the off rate measurement [koff] of a MHC:ligand complex c

cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001606

A cell bound MHC binding assay that uses fluorescence detection to detect direct binding.
Source
IEDB
has super-classes
fluorescence detection binding assay c
cell bound MHC binding assay measuring binding of a MHC:ligand complex c
has part op some fluorescence detection assay c
has_specified_input op some cell c and (has part op some MHC protein complex c)

cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001602

A cell bound MHC binding assay that uses radioactivity detection to detect direct binding.
Source
IEDB
has super-classes
radioactivity detection binding assay c
cell bound MHC binding assay measuring binding of a MHC:ligand complex c
has part op some radioactivity detection c
has_specified_input op some cell c and (has part op some MHC protein complex c)

cell co-culturingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000153

A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
Source
OBI branch derived
Example
Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
has super-classes
material processing c
(has_specified_input op some cell c) and (has_specified_input op min 2)
has_specified_input op some culture medium c
has_specified_output op some cultured cell population c
achieves_planned_objective op some material transformation objective c

cell collectingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001483

A planned process that collects cells from culture.
Source
MO_982 harvest
has super-classes
material component separation c
has_specified_input op some cultured cell population c
has_specified_output op some material entity c and (has grain op some cell c)
achieves_planned_objective op some material separation objective c

cell component comparison designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001205

A study design that compares samples from different cell components.
Source
MO_1019 cell_component_comparison_design
has super-classes
study design c
has part op some cellular feature identification objective c
has part op some study design independent variable c and (is about op some cellular_component c)

cell culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001876

A material entity comprised of cultured cells and the media in which they are being propagated or stored.
A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored.
Source
OBI-CLO Alignment Working Group (Spring 2013)
has super-classes
processed material c
has part op some cultured cell c
has part op some culture medium c or cell freezing medium c
has sub-classes
cell line culture c, primary cell culture c

cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001341

An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c

cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001319

An assay of epitope specific interferon-gamma production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-gamma production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific interferon-gamma production by T cells c

cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001220

An assay of epitope specific interleukin-10 production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-10 production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific interleukin-10 production by T cells c

cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001301

An assay of epitope specific interleukin-16 production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-16 production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific interleukin-16 production by T cells c

cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001216

An assay of epitope specific interleukin-2 production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-2 production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific interleukin-2 production by T cells c

cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001384

An assay of epitope specific interleukin-3 production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-3 production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific interleukin-3 production by T cells c

cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001241

An assay of epitope specific interleukin-4 production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-4 production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific interleukin-4 production by T cells c

cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001273

An assay of epitope specific interleukin-5 production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-5 production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific interleukin-5 production by T cells c

cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001413

An assay of epitope specific interleukin-6 production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-6 production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific interleukin-6 production by T cells c

cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001270

An assay of epitope specific transforming growth factor-beta production by T cells that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c

cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001452

A T cell epitope specific tumor necrosis factor production assay that uses a cell culture analyte detection bioassay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c and (has part op some reporter cell line analyte detection bioassay c)
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c

cell culture expansionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001147

a processual entity that results in the increase of cell numbers
Source
MO_758 grow
has super-classes
material processing c
(has_specified_input op some cultured cell population c) and (has_specified_output op some cultured cell population c)
achieves_planned_objective op some material transformation objective c

cell culture splittingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600037

The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.
Source
OBI branch derived
Example
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
has super-classes
material component separation c
has_specified_input op some cultured cell population c
has_specified_output op some cultured cell population c
achieves_planned_objective op some portioning objective c

cell culture supernatantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1000023

Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell.
Source
GROUP: IEDB
Example
solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615
has super-classes
processed material c
is_specified_output_of op some isolation of cell culture supernatant c
derives from op some culture medium c

cell cyclec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0007049

The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
has super-classes
biological_process c

cell cycle designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001409

A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
Source
MO_822 cell_cycle_design
has super-classes
study design c
has part op some cellular feature identification objective c and (is about op some cell cycle c)

cell cycle synchronizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000413

a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
Source
Bjoern Peters and Nicole Washington
Example
Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs.
has super-classes
material processing c
has_specified_input op some cultured cell population c
has_specified_output op some cultured cell population c
achieves_planned_objective op some material transformation objective c

cell differentiation designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001429

A study design that assays events associated with cell development or differentiation.
Source
MO_892 development_or_differentiation_design
has super-classes
study design c
has part op some cellular feature identification objective c and (is about op some cellular developmental process c)

cell fixationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600021

a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time
Source
OBI branch derived
Example
http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus
has super-classes
material processing c
has_specified_input op some cell c and (located in op some specimen c)
has_specified_input op some molecular entity c or chemical solution c
achieves_planned_objective op some material transformation objective c

cell freezing mediumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001912

A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
has super-classes
processed material c

cell harvesterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001119

A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some cell transfer function c

cell killingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0001906

Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
has super-classes
biological_process c
has sub-classes
T cell mediated cytotoxicity c, complement-dependent cytotoxicity c, cytotoxic T cell degranulation c

Cell Lab Quanta SCc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400018

A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells.
Source
http://www.beckmancoulter.com/cell-lab
has super-classes
flow cytometer analyzer c

cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000031

A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
has super-classes
secondary cultured cell population c
has grain op some cell line cell c
has grain op only cell line cell c
has sub-classes
immortal cell line c, mortal cell line c

cell line cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000001

A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
has super-classes
secondary cultured cell c
(is_specified_output_of op some establishing cell line c) or (derives from op some is_specified_output_of op some establishing cell line c)
derives from op some primary cultured cell c
has sub-classes
immortal cell line cell c, mortal cell line cell c

cell line culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001911

A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored.
A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored.
Source
OBI-CLO Alignment Working Group (Spring 2013)
has super-classes
cell culture c
has part op some cell line cell c

cell line immortalizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000877

an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line
A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line.
Source
OBI
Example
Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
has super-classes
establishing cell line c
has part op some immortalizing cell line transformation c
has_specified_output op some immortal cell line c

cell lysatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1000036

a cell lysate is a material entity which is output of a cell lysis process
Source
GROUP: PSI
Example
The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932
has super-classes
processed material c
is_specified_output_of op some cell lysis c
derives from op some cell c

cell lysate MHC binding assay measuring binding of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001579

A MHC binding qualitative binding to ligand assay using MHC in a cell lysate.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a MHC:ligand complex c and (has_specified_input op some cell lysate c and (has part op some MHC protein complex c))
has super-classes
assay measuring qualitiative binding of a MHC:ligand complex c
has sub-classes
cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection c, cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection c

cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001544

A cell lysate MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some cell lysate c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
radioactivity detection binding assay c
assay measuring the dissociation constant [KD] of a MHC:ligand complex c

cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001567

A cell lysate MHC ligand binding off rate measurement (koff) determination assay that uses radioactivity detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the off rate measurement [koff] of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some cell lysate c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value hertz)
has super-classes
radioactivity detection binding assay c
assay measuring the off rate measurement [koff] of a MHC:ligand complex c

cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001565

A cell lysate MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the half life of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some cell lysate c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value minute)
has super-classes
radioactivity detection binding assay c
assay measuring the half life of a MHC:ligand complex c

cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001516

A cell lysate MHC ligand binding half maximal effective concentration (EC50) determination assay that uses radioactivity detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some cell lysate c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
radioactivity detection binding assay c
assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex c

cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001519

A cell lysate MHC binding assay that uses fluorescence detection to detect direct binding.
Source
IEDB
has super-classes
fluorescence detection binding assay c
cell lysate MHC binding assay measuring binding of a MHC:ligand complex c
has part op some fluorescence detection assay c
has_specified_input op some cell lysate c and (has part op some MHC protein complex c)

cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001556

A cell lysate MHC binding assay that uses radioactivity detection to detect direct binding.
Source
IEDB
has super-classes
radioactivity detection binding assay c
cell lysate MHC binding assay measuring binding of a MHC:ligand complex c
has part op some radioactivity detection c
has_specified_input op some cell lysate c and (has part op some MHC protein complex c)

cell lysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302894

cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock.
Source
adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis]
Example
PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41.
has super-classes
killing c
has_specified_input op some cell c or cultured cell population c

cell pelletc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1000024

A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension
Source
GROUP: CEBS
GROUP: OBI Biomaterial Branch
Example
Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214
has super-classes
processed material c
is_specified_output_of op some centrifugation c
derives from op some cultured cell population c or bronchial alveolar lavage c

cell permeabilizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600033

A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
Source
OBI branch derived
Example
Electroporation of HeLa cells to allow transfection with pUC19.
has super-classes
material processing c
has_specified_input op some cell c
has_specified_output op some cell c
achieves_planned_objective op some material transformation objective c
has sub-classes
electroporation c

cell proliferationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0008283

The multiplication or reproduction of cells, resulting in the expansion of a cell population.
has super-classes
biological_process c
has sub-classes
T cell proliferation c

cell proliferation assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000891

A cytometry assay which measures the degreee to which input cells are replicating.
Source
IEDB
Example
Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
is equivalent to
cytometry assay c and ((realizes op some evaluant role c and (inheres in op some cell c)) and (has_specified_input op some cell c)) and (has_specified_output op some is about op some cell proliferation c)
has super-classes
cytometry assay c
has sub-classes
BrdU incorporation assay c, tritiated thymidine incorporation assay c

cell sorter collection tubec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400020

Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
LSR2 collection tube
has super-classes
test tube c

cell specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001468

A specimen primarily composed of cells collected from a multicellular organism or a cell culture
Source
MO_612 cell
has super-classes
specimen c
has grain op some cell c
has role op some specimen role c
has sub-classes
lymph node cell specimen c, splenocyte specimen c

cell transfer functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001043

is a transfer function that displaces cells from one place to another
Example
A cell harvester has a cell transfer function.
has super-classes
transfer function c

cell type comparison designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001411

A study design that compares cells of different type, for example different cell lines.
Source
MO_764 cell_type_comparison_design
has super-classes
study design c
has part op some cellular feature identification objective c
has part op some study design independent variable c and (is about op some cell c)

cell-cell binding detection by flow cytometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000975

A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels.
Source
IEDB
Example
Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates.
is equivalent to
cytometry assay c and (has part op some flow cytometry assay c) and (has_specified_output op some is about op some binding c)
has super-classes
fluorescence detection binding assay c
cytometry assay c

cell-cell killing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000882

A cytometry assay that monitors a cell population to track how many are killed by other cells.
Source
IEDB
Example
Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
is equivalent to
cytometry assay c and (has_specified_input op some cell c) and (has_specified_output op some is about op some cell killing c)
has super-classes
cytometry assay c
has sub-classes
in vitro cell killing assay c, in vivo cell killing assay c

cellular developmental processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0048869

A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
has super-classes
biological_process c

cellular feature identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000219

Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
has super-classes
biological feature identification objective c

cellular processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0009987

Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
has super-classes
biological_process c
has sub-classes
chromatin remodeling c, ion channel activity c

cellular process designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001365

A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
Source
MO_810 cellular_process_design
has super-classes
study design c
has part op some cellular feature identification objective c and (is about op some cellular process c)

cellular qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001396

A monadic quality of continuant that exists at the cellular level of organisation.
has super-classes
quality of a single physical entity c
has sub-classes
ploidy c

cellular response to DNA damage stimulusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0006974

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
has super-classes
response to stimulus c

cellular structure feature identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001691

is an objective specification which aims to discover cellular structure properties
Source
OBI group
has super-classes
biological feature identification objective c

cellular_componentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0005575

The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
has super-classes
material entity c
has sub-classes
chromosome c, membrane-bounded organelle c

center calculation data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200181

A center calculation data transformation is a data transformation that has objective of center calculation.
Source
PERSON: James Malone
is equivalent to
(has_specified_output op some center value c) or (achieves_planned_objective op some center calculation objective c)
has super-classes
data transformation c
has sub-classes
arithmetic mean calculation c, geometric mean calculation c, median calculation c, mode calculation c, quantile transformation c, skewness calculation c

center calculation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200177

A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
Source
PERSON: James Malone
Example
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
has super-classes
data transformation objective c

center valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000674

A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
is equivalent to
is_specified_output_of op some center calculation data transformation c
has super-classes
data item c

centrally registered identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000578

An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
Source
Original proposal from Bjoern, discussions at IAO calls
Example
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has super-classes
information content entity c
has part op some centrally registered identifier symbol c
has part op some denotes op some centrally registered identifier registry c

centrally registered identifier registryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000579

A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
Source
Original proposal from Bjoern, discussions at IAO calls
Example
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
has super-classes
data set c

centrally registered identifier symbolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000577

A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
Source
Original proposal from Bjoern, discussions at IAO calls
Example
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has super-classes
symbol c
part of op some centrally registered identifier c
has sub-classes
GenBank ID c, PubMed ID c, digital object identifier c, grant identifier c, individual organism identifier c, investigation identifier c, specimen identifier c

centrifugationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302886

centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
Source
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
Example
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c
has participant op some centrifuge c

centrifugec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400106

A device with a rapidly rotating container that applies centrifugal force to its contents
Source
http://en.wikipedia.org/wiki/Centrifuge
has super-classes
measurement device c
material separation device c
has part op some has function op some contain function c
has function op some measure function c
has function op some material separation function c and (realized in op only centrifugation c)
has sub-classes
microcentrifuge c

centrifuge pellet rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000029

pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material..
Source
OBI
Example
Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
has super-classes
role c
inheres in op some material entity c
realized in op only centrifugation c

centroid mass spectrumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200064

A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data.
Source
centroid mass spectrum
has super-classes
mass spectrometry analysis c
achieves_planned_objective op some spectrum analysis objective c

cerebellumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002037

Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
has super-classes
multi-tissue structure c

cerebellum specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002538

A specimen that is derived from cerebellum.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some cerebellum c))
has super-classes
specimen from organism c

cerebral cortexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000956

The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
has super-classes
anatomical cluster c

cerebral cortex specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002536

A specimen that is derived from cerebral cortex.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some cerebral cortex c))
has super-classes
specimen from organism c

cerebrospinal fluidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001359

A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
has super-classes
organism substance c

cerebrospinal fluid specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002502

A specimen that is derived from cerbrospinal fluid.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some cerebrospinal fluid c))
has super-classes
specimen from organism c

cervical dislocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302896

cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion
Source
OBI branch
Example
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3
has super-classes
animal euthanization c

chain termination sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000695

is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position
Source
adapted from wikipedia
Example
PMID: 271968. DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7.
has super-classes
DNA sequencing by synthesis c
has_specified_input op some PCR product c
has participant op some ABI 377 automated sequencer c or Li-Cor 4300 DNA Analysis System c

characteristic path length calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200063

Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices
Source
PERSON: Tina Hernandez-Boussard
has super-classes
mass spectrometry analysis c
achieves_planned_objective op some spectrum analysis objective c

charge platec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400019

Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
LSR2 charge plate
has super-classes
device c
has function op some excitation function c
has function op some transfer function c

chart recorderc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000605

The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069
has super-classes
chromatography device c

chemical cleavagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000943

chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent
Source
RNA ontology group
Example
PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. Biochimie. 2010 Feb 18.
has super-classes
material processing c
has_specified_input op some specimen c
has_specified_input op some molecular entity c and (has role op some reagent role c)
achieves_planned_objective op some material transformation objective c

chemical solutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302729

A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute.
Source
GROUP: OBI Biomaterial Branch
Example
PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution.
is equivalent to
(has part op some scattered molecular aggregate c and (has role op some solvent role c)) and (has part op some scattered molecular aggregate c and (has role op some solute role c))
has super-classes
material entity c
has sub-classes
phosphate buffered saline solution c

chemokine (C-C motif) ligand 1 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071610

The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-C motif) ligand 1 production by T cells c

chemokine (C-C motif) ligand 17 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0044809

The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c

chemokine (C-C motif) ligand 19 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097388

The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-C motif) ligand 19 production by T cells c

chemokine (C-C motif) ligand 21 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097389

The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-C motif) ligand 21 production by T cells c

chemokine (C-C motif) ligand 22 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071924

The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-C motif) ligand 22 production by T cells c

chemokine (C-C motif) ligand 4 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071606

The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-C motif) ligand 4 production by T cells c

chemokine (C-C motif) ligand 5 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071609

The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific RANTES production by T cells c

chemokine (C-X-C motif) ligand 12 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097390

The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-X-C motif) ligand 12 production by T cells c

chemokine (C-X-C motif) ligand 13 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097391

The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-X-C motif) ligand 13 production by T cells c

chemokine (C-X-C motif) ligand 16 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097392

The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-X-C motif) ligand 16 production by T cells c

chemokine (C-X-C motif) ligand 9 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0035393

The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c

chemokine productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032602

The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
IP-10 production c, chemokine (C-C motif) ligand 1 production c, chemokine (C-C motif) ligand 17 production c, chemokine (C-C motif) ligand 19 production c, chemokine (C-C motif) ligand 21 production c, chemokine (C-C motif) ligand 22 production c, chemokine (C-C motif) ligand 4 production c, chemokine (C-C motif) ligand 5 production c, chemokine (C-X-C motif) ligand 12 production c, chemokine (C-X-C motif) ligand 13 production c, chemokine (C-X-C motif) ligand 16 production c, chemokine (C-X-C motif) ligand 9 production c, macrophage inflammatory protein-1 alpha production c, macrophage inflammatory protein-1 gamma production c, monocyte chemotactic protein-1 production c

chi square testc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200200

The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough.
has super-classes
statistical hypothesis test c
achieves_planned_objective op some statistical hypothesis test objective c

chimerac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100014

An organism which contains cells or tissues with a different genotype
Source
GROUP: OBI
has super-classes
organism c

ChIP assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001954

An assay in which protein-DNA complexes are extracted from short regions of chromatin and are reversibly cross linked, immunoprecipitated with antibodies or tags, purified, and amplified with the aim of analysis gene- and promoter-specific known targets
Source
adapted from CHS protocols, wikipedia, life tech, ChIP-seq term definition
Example
PMID: 6379641 Gilmour & Lis. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4275-9. and can be found linked from here:
has super-classes
assay using chromatin immunoprecipitation c
epigenetic modification assay c
has part op some immunoprecipitation c
realizes op some analyte role c and (role of op some deoxyribonucleic acid c)
has_specified_input op some specimen c and ((has part op some deoxyribonucleic acid c) and (has part op some protein complex c))
has_specified_output op some information content entity c and (is about op some chromatin remodeling c or regulation of molecular function, epigenetic c or sequence-specific DNA binding c or transcription factor binding site c)
achieves_planned_objective op some epigenetic modification identification objective c
achieves_planned_objective op some protein and DNA interaction identification objective c

chip spotting devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001049

A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray.
Source
United States Patent 7416705
has super-classes
device c
has function op some transfer function c

ChIP-chip assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001248

an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis.
Philippe Rocca-Serra
Source
WEB: http://en.wikipedia.org/wiki/ChIP-on-chip
has super-classes
assay using chromatin immunoprecipitation c
has part op some immunoprecipitation c
realizes op some analyte role c and (role of op some deoxyribonucleic acid c)
has_specified_input op some specimen c and (has part op some deoxyribonucleic acid c) and (has part op some protein complex c)
has_specified_output op some information content entity c and (is about op some chromatin remodeling c or regulation of molecular function, epigenetic c or sequence-specific DNA binding c or transcription factor binding site c)
achieves_planned_objective op some protein and DNA interaction identification objective c
has participant op some DNA microarray c
has sub-classes
ChIP-chip by SNP array assay c, ChIP-chip by tiling array assay c, DNA methylation profiling by ChIP-chip assay c, histone modification identification by ChIP-chip assay c, transcription factor binding site identification by ChIP-chip assay c

ChIP-chip by SNP array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001221

An assay where chromatin immunoprecipitation (ChIP) is used in combination with SNP microarray technology
Source
EFO_0002764 ChIP-chip by SNP array
has super-classes
ChIP-chip assay c
has participant op some SNP microarray c

ChIP-chip by tiling array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001419

An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology
Source
EFO_0002762 ChIP-chip by tiling array
has super-classes
ChIP-chip assay c
has participant op some tiling microarray c

ChIP-chip by tiling array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001417

A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays.
Source
Group: ArrayExpress production team
has super-classes
ChIP-chip design c
is concretized as op some realized in op only (has part op some ChIP-chip by tiling array assay c) and (has participant op some tiling microarray c)

ChIP-chip designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001403

A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays.
Source
MO_933 binding_site_identification_design
has super-classes
protein binding site identification design c
has part op some protein and DNA interaction identification objective c
has part op some study design independent variable c and (is about op some immunoglobulin complex, circulating c)
is concretized as op some realized in op some (has part op some ChIP-chip assay c) and (has participant op some DNA microarray c)
has sub-classes
ChIP-chip by tiling array design c

ChIP-seq assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000716

an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
Source
adapted from Wikipedia
Example
PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9.
has super-classes
assay using chromatin immunoprecipitation c
epigenetic modification assay c
sequencing assay c
has part op some DNA sequencing c
has part op some immunoprecipitation c
has part op some library preparation c
realizes op some analyte role c and (role of op some deoxyribonucleic acid c)
has_specified_input op some specimen c and ((has part op some deoxyribonucleic acid c) and (has part op some protein complex c))
has_specified_output op some DNA sequence data c
has_specified_output op some information content entity c and (is about op some chromatin remodeling c or regulation of molecular function, epigenetic c or sequence-specific DNA binding c or transcription factor binding site c)
achieves_planned_objective op some epigenetic modification identification objective c
achieves_planned_objective op some protein and DNA interaction identification objective c
has participant op some DNA sequencer c
has sub-classes
chromatin immunoprecipitation with exonuclease sequencing assay c, histone modification identification by ChIP-Seq assay c, transcription cofactor activity region identification by ChIP-Seq assay c, transcription factor binding site identification by ChIP-Seq assay c

ChIP-seq designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001258

A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications.
Source
http://en.wikipedia.org/wiki/Chip-Sequencing
has super-classes
protein binding site identification design c
has part op some epigenetic modification identification objective c
has part op some protein and DNA interaction identification objective c
is concretized as op some realized in op some (has part op some ChIP-seq assay c) and (has participant op some DNA sequencer c)

chromatin immunoprecipitationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_00001975

An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics.
Source
OBI
Example
Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method.
has super-classes
immunoprecipitation c

chromatin immunoprecipitation with exonuclease sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001925

A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing.
Source
Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082]
Example
Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082]
has super-classes
ChIP-seq assay c
has part op some cross linking c
has part op some specific enzymatic cleavage c
realizes op some evaluant role c and (role of op some protein complex c)
has_specified_output op some DNA sequence data c
has participant op some sonicator c

chromatin interaction analysis by paired-end tag sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001848

An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide.
Source
http://en.wikipedia.org/wiki/ChIA-PET
Example
Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262]
has super-classes
assay using chromatin immunoprecipitation c
sequencing assay c
has part op some DNA sequencing c
has part op some immunoprecipitation c
has part op some cross linking c
has part op some paired-end library preparation c
has_specified_input op some protein complex c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some analyte measurement objective c
achieves_planned_objective op some protein and DNA interaction identification objective c
has participant op some DNA sequencer c

chromatin isolation by RNA purification sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002040

A detection of specific nucleic acids with complementary probes to discover regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing.
Source
Chu et al. (31 August 2011). "Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions". Molecular Cell.
Example
Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111.
has super-classes
detection of specific nucleic acid polymers with complementary probes c

chromatin remodelingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0006338

Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
has super-classes
cellular process c

chromatofocusing columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000515

A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind.
Source
WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209
has super-classes
chromatography column c

chromatography assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001661

A B cell epitope qualitative binding to antibody assay that uses an analytical chromatography assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some analytical chromatography c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001995

A B cell epitope equilibrium association constant (KA) determination assay that uses an analytical chromatography assay.
Source
IEDB
is equivalent to
assay measuring the association constant [KA] of a B cell epitope:antibody complex c and (has part op some analytical chromatography c) and (has_specified_output op some has measurement unit label op value count per nanomolar)
has super-classes
assay measuring the association constant [KA] of a B cell epitope:antibody complex c

chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001996

A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an analytical chromatography assay.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c and (has part op some analytical chromatography c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c

chromatography columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000038

Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
Source
http://en.wikipedia.org/wiki/Column_chromatography
has super-classes
material separation device c
has part op some container c
has function op some material separation function c and (realized in op only preparative chromatography c)
has sub-classes
affinity column c, capillary column c, carbon nanotube column c, chromatofocusing column c, custom made column c, gel permeation column c, glass column c, high temperature column c, ion exchange column c, liquid chromatography column c, normal phase column c, open tubular column c, organic acid column c, packed column c, plunger column c, protein column c, reversed phase column c, size exclusion column c, spin column c, trap column c

chromatography consumablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000601

A chromatography consumable is a consumable that is used in a chromatography experiment.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115
has super-classes
chromatography device c
has sub-classes
chromatography detector filter c, detector lamp c, injector lubricant c, piston-seal c, vial c

chromatography detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000481

A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range.
Source
WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012
has super-classes
chromatography instrument c
has sub-classes
gas chromatography detector c

chromatography detector filterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000592

An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121
has super-classes
chromatography consumable c
has sub-classes
in-line filter c, syringe filter c

chromatography devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000048

a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
Source
http://en.wikipedia.org/wiki/Chromatography
has super-classes
measurement device c
material separation device c
physical store c
has function op some contain function c
has function op some material separation function c
has function op some environment control function c
has function op some measure function c
has sub-classes
chart recorder c, chromatography consumable c, chromatography splitter c, column adapter c, column cartridge c, column compartment c, column connector c, column frit c, column jacket c, gas chromatography equipment c, guard column c, liquid chromatography instrument c, liquid chromatography valve c, needle assembly c, sample injection system c, sample inlet c, transfer line c

chromatography instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000485

Any instrument that is used to carry out a chromatography experiment.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262
has super-classes
material separation device c
has function op some material separation function c
has sub-classes
chromatography detector c, chromatography pump system c, column cartridger c, column heater c, fraction collector c, liquid chromatography autosampler c, solvent mixer c

chromatography pump systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000589

Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
Source
WEB:<http://en.wikipedia.org/wiki/Column_chromatography>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046
has super-classes
chromatography instrument c
has sub-classes
capillary pump system c, flash pump system c, gradient pump system c, isocratic pump system c, nano pump system c, quaternary pump system c, vacuum degasser c

chromatography splitterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000619

An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities.
Source
WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041
has super-classes
chromatography device c

chromium release assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_9999994

An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died.
Source
IEDB
Example
Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
has super-classes
in vitro cell killing assay c
(realizes op some molecular label role c and (inheres in op some chromium-51 c)) and (has_specified_input op some chromium-51 c)
has part op some radioactivity detection c

chromium-51c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_50076

A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
has super-classes
molecular entity c

chromosomal substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001150

A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'.
Source
MO_995 chromosomal_substitution
has super-classes
genetic transformation c

chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0005694

A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
has super-classes
cellular_component c

chromosome conformation identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001917

A molecular feature identification objective that aims to determine spatial organization of chromatin.
Source
Group: Penn Group
has super-classes
molecular feature identification objective c

chromosome organizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0051276

A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
has super-classes
biological_process c

chromosome organization assay by fluorescence in situ hybridizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001683

is an in situ hybridization assay that uses fluorescence as means of detection chromosomal integrity
Example
Duplication of intrachromosomal insertion segments 4q32→q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization.PMID:22384449
is equivalent to
(in situ hybridization c and (has_specified_input op some binding constant c) and (has_specified_output op some data item c and (is about op some chromosome organization c))) and (achieves_planned_objective op some biological feature identification objective c)
has super-classes
in situ hybridization c

circularc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000988

A quality of a nucleotide polymer that has no terminal nucleotide residues.
has super-classes
quality of a single physical entity c

citationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000301

a textual entity intended to identify a particular publication
Example
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
has super-classes
textual entity c
is about op some document c

class discovery data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200175

A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
Source
PERSON: James Malone
is equivalent to
(has_specified_output op some clustered data set c) or (achieves_planned_objective op some class discovery objective c)
has super-classes
data transformation c
has sub-classes
dimensionality reduction c, discriminant function analysis c, hierarchical clustering c, k-means clustering c, k-nearest neighbors c, linear discriminant functional analysis c, principal component regression c, self-organizing map c, similarity calculation c

class discovery objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200178

A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
has super-classes
data transformation objective c

class prediction data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000663

A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
Source
PERSON: James Malone
is equivalent to
(has_specified_output op some classified data set c) or (achieves_planned_objective op some class prediction objective c)
has super-classes
data transformation c
has sub-classes
discriminant function analysis c, linear discriminant functional analysis c, similarity calculation c, support vector machine c

class prediction objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200179

A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
has super-classes
data transformation objective c

classified data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000023

A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
is equivalent to
is_specified_output_of op some class prediction data transformation c
has super-classes
data set c

classified data visualizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200192

A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type.
has super-classes
data visualization c
has_specified_output op some heatmap c or scatter plot c
has_specified_input op only classified data set c

clinical chemistry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000520

a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism.
Source
adapted from Wikipedia
Example
Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. Mueller T, Schimetta W, Dieplinger B, Loeffler P, Rehm M, Kreimeier U, Poelz W, Haltmayer M. Clin Chem Lab Med. 2008;46(4):558-62. PMID: 18605936
has super-classes
analyte assay c
realizes op some evaluant role c and (role of op some material entity c)
realizes op some analyte role c and (role of op some scattered molecular aggregate c)
achieves_planned_objective op some analyte measurement objective c

clinical historyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000015

A series of statements representing health-relevant qualities of a patient and of a patient's family.
has super-classes
information content entity c

clinical history designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001337

A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
Source
MO_832 clinical_history_design
has super-classes
study design c
has part op some organism feature identification objective c and (is about op some clinical history c)

clinical research coordinator rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000032

a worker role comprised of handling the administrative duties of a trial or study.
has super-classes
worker role c

clinical study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500001

Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
Source
Clinical Research Glossary Version 4.0 CDICS glossary group
Example
PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
has super-classes
study design c

cloacal specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000909

A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium.
Source
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
Example
type of sample used in the PCIRN influenza network
has super-classes
specimen c
has role op some specimen role c

cloning insert rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000416

cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
Source
OBII and Wikipedia
has super-classes
role c

cloning plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000729

A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site.
is equivalent to
plasmid c and (has role op some cloning vector role c)
has super-classes
plasmid c
cloning vector c

cloning vectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000737

A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
is equivalent to
material entity c and (has role op some cloning vector role c)
has super-classes
processed material c
material to be added c
is_specified_output_of op some material processing c
has sub-classes
cloning plasmid c, yeast artificial chromosome vector c

cloning vector rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000411

A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
Example
pBluescript plays the role of a cloning vector
has super-classes
material to be added role c
(inheres in op some nucleic acid c) and (realized in op only recombinant vector cloning c)

clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000251

A data set which is a subset of data that are a similar to each other in some way.
Source
group:OBI
Example
Cluster of the lymphocytes population.
has super-classes
data set c

clustered data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000648

A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
Example
A clustered data set is the output of a K means clustering data transformation
is equivalent to
is_specified_output_of op some class discovery data transformation c
has super-classes
data set c
has sub-classes
topologically preserved clustered data set c

clustered data visualizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200190

A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
has super-classes
data visualization c
has_specified_output op some dot plot c or histogram c or heatmap c or dendrogram c or scatter plot c
has_specified_input op only clustered data set c
has members
GenePattern HeatMapViewer data visualization ni, GenePattern HierarchicalClusteringViewer data visualization ni

CMCT structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001006

a single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:2422386 and PMID:2446263
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some diethyl pyrocarbonate c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

coagulation analyzerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001095

A device for automatically analyzing blood coagulation in a clinical laboratory.
Source
United States Patent 5439646
has super-classes
measurement device c
has function op some measure function c

coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001500

A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules.
Source
IEDB
has super-classes
assay measuring MHC ligand processing and presentation c
has part op some assay measuring binding of a T cell epitope:MHC:TCR complex c
has_specified_input op some material entity c and (has role op some positive reference substance role c)

cohort rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000252

a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study.
Source
WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.
Example
In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008
has super-classes
biological replicate role c

collecting specimen from organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600005

a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
Source
IEDB
Example
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has super-classes
specimen collection process c
has_specified_input op some organism c
has_specified_output op some specimen c
achieves_planned_objective op some specimen collection objective c
has sub-classes
lavage c

collection of specimensc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002076

A material entity that has two or more specimens as its parts.
Source
OBIB, OBI
Example
Blood cells collected from multiple donors over the course of a study.
is equivalent to
material entity c and (has member op only specimen c) and (has member op min 2 specimen c)
has super-classes
material entity c
has sub-classes
specimens collected in one encounter c, specimens collected longitudinally c, specimens derived from shared ancestor c

colonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001155

Last portion of the large intestine before it becomes the rectum.
has super-classes
material anatomical entity c

colon specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002533

A specimen that is derived from colon.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some colon c))
has super-classes
specimen from organism c

column adapterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000594

An Adapter that enabled the connection of a column to additional devices.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113
has super-classes
chromatography device c

column cartridgec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000532

A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055
has super-classes
chromatography device c

column cartridgerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000549

A chromatography device where the column cartridge is inserted into and stabilised.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054
has super-classes
chromatography instrument c

column chromatography detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000463

There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles.
Source
WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077
has super-classes
measurement device c
has function op some measure function c

column compartmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000545

For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068
has super-classes
chromatography device c

column connectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000478

A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236
has super-classes
chromatography device c
has sub-classes
y-column connector c

column fritc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000602

A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density).
Source
WEB:<http://www.chromatography-online.org/topics/radial/columns.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070
has super-classes
chromatography device c

column heaterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000633

The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure.
Source
WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040
has super-classes
chromatography instrument c

column jacketc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000508

A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276
has super-classes
chromatography device c

column submatrix extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200076

A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
Example
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set.
has super-classes
submatrix extraction c

comet assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302736

a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions.
Source
PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review.
Example
PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay.
has super-classes
assay c
has_specified_input op some cell c
has_specified_input op some agarose gel c
has_specified_output op some information content entity c and (is about op some cellular response to DNA damage stimulus c)
achieves_planned_objective op some assay objective c
has participant op some gel tank c
has participant op some power supply c

comment on investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001898

A textual entity that is about any of the aspects of an investigation worth noting
Source
NIAID GSCID-BRC metadata working group
is equivalent to
textual entity c and (is about op some material entity c and (planned process c or (participates in op some investigation c)) and (part of op some investigation c))
has super-classes
textual entity c

comparative genome hybridization by array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001197

A study design that detects genomic copy number variations using microarray technology.
Source
MO_856 comparative_genome_hybridization_design
has super-classes
study design c
has part op some molecular feature identification objective c
is concretized as op some realized in op some (has part op some comparative genomic hybridization by array assay c) and (has participant op some DNA microarray c)

comparative genomic hybridization by array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001393

An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
Philippe Rocca-Serra
Source
EFO_0000749: comparative genomic hybridization by array
has super-classes
genotyping assay c
realizes op some analyte role c and (role of op some deoxyribonucleic acid c)
has_specified_input op some specimen c and (has part op some deoxyribonucleic acid c)
has_specified_output op some genotype information c
achieves_planned_objective op some molecular feature identification objective c
has participant op some DNA microarray c

comparative phenotypic assessmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001546

Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference
Source
Philly workshop 2011
has super-classes
drawing a conclusion based on data c
drawing a conclusion c
has_specified_input op some measurement datum c and (is about op some organism c or (part of op some organism c))
has_specified_output op some conclusion textual entity c and (is about op some (disposition c or quality c) and (inheres in op some organism c or (part of op some organism c)))

comparing prediction to measurementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001932

A planned process in which predicted values for some thing are compared to measured values for that thing.
has super-classes
planned process c
has part op some process c and (has_specified_output op some measurement datum c and (is about op some entity c and (inverse is about op some predicted value c)))
has_specified_input op some predicted value c

competitive binding reference ligand rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001955

A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target.
Source
Bjoern Peters
Example
The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion.
has super-classes
positive reference substance role c

competitive inhibition of binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001593

A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material.
Source
IEDB
Example
Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide.
has super-classes
binding assay c
has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)
has sub-classes
antibody cross-blocking assay c

complement-dependent cytotoxicityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097278

Lysis of a cell resulting from triggering of the complement cascade. An example can be seen with complement activation and subsequent lysis of a bacterial cell as a result of the binding of IgM to the cell surface followed by the binding of complement proteins to that antibody.
has super-classes
cell killing c
has sub-classes
B cell epitope specific complement-dependent cytotoxicity c

complementary nucleotide probe rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000857

A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
Example
A primer in a PCR reaction. A probe on an Affymetrix chip.
has super-classes
role c
inheres in op some nucleic acid c
has sub-classes
primer role c

complete linkage hierarchical clusteringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200044

an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster.
Source
PERSON: Elisabetta Manduchi
has super-classes
agglomerative hierarchical clustering c

complete nutrient rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000162

A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment.
Example
Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm
has super-classes
nutrient role c
has sub-classes
feed role c

compliance rulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500023

a compliance rule is a rule which ensures a compliance process occurs
Source
PRS
has super-classes
rule c
has sub-classes
standard compliance rule c

compound treatment designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000951

an intervention design in which the treatment is the administration of a compound
Source
MO_555 compound_treatment_design
is equivalent to
study design c and (has part op some study design independent variable c and (is about op some study intervention c and administration of material to specimen c))
has super-classes
intervention design c
has sub-classes
dose response design c

computation run timec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001913

computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency.
Source
PRS,AGB
Example
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. See Table 4
has super-classes
time measurement datum c
is duration of op some data transformation c

computed tomography scannerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000982

An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation.
Source
http://en.wikipedia.org/wiki/X-ray_computed_tomography
has super-classes
image creation device c
has function op some image acquisition function c

computerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400107

A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
Source
http://en.wikipedia.org/wiki/Computer
Example
Apple PowerBook, Dell OptiPlex
has super-classes
device c
has function op some information processor function c
has sub-classes
acquisition computer c, computer cluster c

computer clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001092

A group of linked computers, working together closely so that in many respects they form a single computer.
Source
http://en.wikipedia.org/wiki/Cluster_(computing)
has super-classes
computer c

concentratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600041

a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material
Source
OBI branch derived
Example
Evaporation of the solution containing DNA to increase the concentration of the DNA molecules
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c

concentration unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000051

A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
has super-classes
measurement unit label c
has members
colony forming unit per volume ni, gram per deciliter ni, gram per liter ni, mass percentage ni, mass volume percentage ni, microgram per liter ni, micromolar ni, milligram per milliliter ni, milliliter per liter ni, millimolar ni, molar ni, nanomolar ni, pH ni, picomolar ni, volume percentage ni

conclusion based on datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001909

An information content entity that is inferred from data.
Source
Group:2013 Philly Workshop group
Example
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
has super-classes
information content entity c
is_supported_by_data op some data item c
is_specified_output_of op some drawing a conclusion based on data c
has sub-classes
conclusion textual entity c
is in domain of
is_supported_by_data op

conclusion textual entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000144

A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
Example
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has super-classes
textual entity c
conclusion based on data c
is_supported_by_data op some data item c
is_specified_output_of op some drawing a conclusion based on data c

conditional specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000001

a directive information entity that specifies what should happen if the trigger condition is fulfilled
Source
OBI branch derived
OBI_0000349
has super-classes
directive information entity c
has sub-classes
adverse event trigger c, rule c, time trigger c

confocal microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001079

A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane.
Source
http://en.wikipedia.org/wiki/Confocal_microscopy
has super-classes
microscope c
has function op some measure function c
has sub-classes
laser scanning confocal microscope c, programmable array microscope c, spinning-disk confocal microscope c

connection functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000388

A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another.
Example
An electricity cable
has super-classes
function c

connective tissue growth factor productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032601

The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

consume data functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000455

Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
has super-classes
function c
function of op some material entity c

contact representative rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001687

A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
has super-classes
role c
inheres in op some Homo sapiens c

contact to pathogen carrying biological vectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110114

a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result
Source
IEDB
has super-classes
environmental proximity to infectious agent c

contain functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000370

A contain function is a function to constrain a material entities location in space
Example
A syringe, a beaker
has super-classes
function c
has sub-classes
containing a specimen function c

containerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000967

A device that can be used to restrict the location of material entities over time
is equivalent to
has function op some contain function c
has super-classes
device c
has sub-classes
animal cage c, cryostat c, flow cell c, microtiter plate c, paraffin oven c, photomultiplier tube c, physical store c, specimen container c, supernatant collection system harvesting frame c, syringe pump c, test tube c, vacuum oven c, waste tank c

containing a specimen functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002087

A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay.
Source
Duke Biobank, OBIB
has super-classes
contain function c

contigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000149

A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
has super-classes
sequence_assembly c

contig N50c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001941

N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.
Source
adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
Example
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
has super-classes
N50 c
is about op some contig c and (is_specified_output_of op some sequence assembly process c)

continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000002

An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
entity c
has sub-classes
generically dependent continuant c, independent continuant c, specifically dependent continuant c
is in domain of
is_proxy_for op, participates in op
is in range of
has participant op, is_proxy_for op
is disjoint with
occurrent c

continuant fiat boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000140

b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
immaterial entity c
has sub-classes
one-dimensional continuant fiat boundary c, two-dimensional continuant fiat boundary c, zero-dimensional continuant fiat boundary c
is disjoint with
spatial region c, site c

continuous wave NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000486

Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned).
Source
WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283
has super-classes
NMR instrument c

continuum mass spectrumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200062

A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion.
Source
PERSON: Tina Boussard
has super-classes
mass spectrometry analysis c
achieves_planned_objective op some spectrum analysis objective c

contour plotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000057

Source
OBI_0000246
group:Flow Cytometry community
Example
Contour plot of SSC-H, FSC-H, and FL1-H.
has super-classes
graph c

contract research organization rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000020

a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution
has super-classes
worker role c

cool functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000387

A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
has super-classes
function c

copy number variation profilingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000537

copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping.
Example
Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. de Ståhl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP. Hum Mutat. 2008 Mar;29(3):398-408. PMID: 18058796
has super-classes
assay c
has_specified_output op some measurement datum c and (is about op some genetic characteristics information c)
achieves_planned_objective op some assay objective c

copyright sectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000330

A document part that describes legal restrictions on making or distributing copies of the document
Example
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
has super-classes
document part c

core promoter bindingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0001047

Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
has super-classes
binding c

coronary arteryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001621

An artery that supplies the myocardium.
has super-classes
material anatomical entity c

coronary artery specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002540

A specimen that is derived from coronary artery.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some coronary artery c))
has super-classes
specimen from organism c

correction objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200168

A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
Source
PERSON: James Malone
PERSON: Melanie Courtot
Example
Type I error correction
has super-classes
data transformation objective c
has sub-classes
background correction objective c, error correction objective c

correlation study objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200196

A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables.
has super-classes
data transformation objective c

cortex of kidneyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001225

Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
has super-classes
material anatomical entity c

cortex of kidney specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002531

A specimen that is derived from cortex of kidney.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some cortex of kidney c))
has super-classes
specimen from organism c

cosine transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200017

A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html.
Source
WEB: http://mathworld.wolfram.com/Cosine.html
Example
cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

country namec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001627

A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
Source
NIAID GSCID-BRC metadata working group
Website: http://en.wikipedia.org/wiki/Country
has super-classes
textual entity c
denotes op some geographic location c

creating a mixture of molecules in solutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000685

is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
Source
PERSON: Helen Parkinson
Example
The production of PBS
has super-classes
material combination c
has_specified_input op some material entity c
has_specified_output op some chemical solution c
achieves_planned_objective op some material transformation objective c
achieves_planned_objective op some material combination objective c

cross blocking assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001648

A B cell epitope qualitative binding to antibody assay that uses an antibody cross-blocking assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some antibody cross-blocking assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

cross linkingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000800

A process in which bonds are created that link one polymer to another
Source
http://en.wikipedia.org/wiki/Cross-link
Example
cross linking can be used as a probe to link proteins together, to check protein protein interactions
has super-classes
material processing c
has_specified_output op some molecular entity c
achieves_planned_objective op some material transformation objective c

cross over designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500003

a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
Source
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
Example
PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
has super-classes
repeated measure design c
has sub-classes
n-to-1 design c

cross validation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200188

A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
Source
WEB: http://en.wikipedia.org/wiki/Cross_validation
has super-classes
partitioning objective c

cross-linking immunoprecipitation high-throughput sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001858

An assay that employs UV-crosslinking between RNA and the protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput used for screening for RNA sequences that interact with a particular RNA-binding protein.
Source
Licatalosi et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 2008 Nov 27 456: 464-469 [PMID:18978773]
Example
Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288]
has super-classes
analyte assay c
sequencing assay c
has part op some immunoprecipitation c
has part op some library preparation c
has part op some cross linking c
has part op some RNA sequencing c
has_specified_input op some protein complex c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some analyte measurement objective c
achieves_planned_objective op some protein and RNA interaction identification objective c
has participant op some DNA sequencer c
has participant op some sonicator c
has sub-classes
individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay c

crossover population rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000161

a role realized when a participant serves as reference to itself
has super-classes
reference subject role c

cryofixation devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001074

A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy.
Source
http://en.wikipedia.org/wiki/Cryofixation
has super-classes
device c
has function op some specimen fixation function c

cryostatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001072

A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION
Source
http://en.wikipedia.org/wiki/Cryostat
has super-classes
container c
environmental control device c
has function op some contain function c
has function op some mechanical function c
has function op some cool function c

culture mediumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000079

a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
Source
OBI
Example
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has super-classes
processed material c
has sub-classes
Dulbecco's modified Eagle medium c

cultured adherent cell populaitonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110043

A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role.
Source
IEDB
is equivalent to
cultured cell population c and (is_specified_output_of op some isolation of adherent cells c)
has super-classes
cultured cell population c

cultured antigen presenting cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110106

a cell culture including cells that have an antigen presentation function
Source
IEDB
Example
A culture of PBMCs. A culture of Hela cells.
is equivalent to
cultured immune cell population c and (has grain op some cell c and (has function op some antigen presentation function c))
has super-classes
cultured immune cell population c

cultured CD3+ T cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110047

A T cell population characterized by expressing the CD3 molecule on its surface.
Source
IEDB
is equivalent to
cultured immune cell population c and (has grain op some cell c and (has part op some CD3 subunit with immunoglobulin domain c))
has super-classes
cultured immune cell population c

cultured CD3- T cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110048

A T cell population characterized by not expressing the CD3 molecule on its surface.
Source
IEDB
is equivalent to
cultured immune cell population c and (has grain op some cell c and (not (has part op some CD3 subunit with immunoglobulin domain c)))
has super-classes
cultured immune cell population c

cultured CD4- T cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110050

A T cell population characterized by not expressing the CD4 molecule on its surface.
Source
IEDB
is equivalent to
cultured immune cell population c and (has grain op some cell c and (not (has part op some CD4 molecule c)))
has super-classes
cultured immune cell population c
has sub-classes
cultured CD4-/CD8- T cell population c

cultured CD4-/CD8- T cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110052

A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface.
Source
IEDB
is equivalent to
cultured immune cell population c and (has grain op some cell c and (not (has part op some CD8 receptor c)) and (not (has part op some CD4 molecule c)))
has super-classes
cultured CD4- T cell population c
cultured CD8- T cell population c

cultured CD8- T cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110051

A T cell population characterized by not expressing the CD8 molecule on its surface.
Source
IEDB
is equivalent to
cultured immune cell population c and (has grain op some cell c and (not (has part op some CD8 receptor c)))
has super-classes
cultured immune cell population c
has sub-classes
cultured CD4-/CD8- T cell population c

cultured cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000010

A cell in vitro that is or has been maintained or propagated as part of a cell culture.
has super-classes
experimentally modified cell in vitro c
(is_specified_output_of op some establishing cell culture c) or (derives from op some is_specified_output_of op some establishing cell culture c)
has sub-classes
primary cultured cell c, secondary cultured cell c

cultured cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100060

A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
Source
PERSON:Matthew Brush
Example
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has super-classes
processed material c
is_specified_output_of op some maintaining cell culture c
has grain op some cultured cell c
has grain op only cultured cell c
has sub-classes
cultured adherent cell populaiton c, cultured clonal cell population c, cultured immune cell population c, primary cultured cell population c, secondary cultured cell population c

cultured clonal cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100063

A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical.
Source
GROUP: OBI Biomaterial Branch
Example
cell cut Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557
has super-classes
cultured cell population c

cultured effector T cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110107

A cell culture including cells that have an effector T cell function
Source
IEDB
Example
A culture of cytotoxic CD8+ T cells.
is equivalent to
cultured immune cell population c and (has grain op some T cell c and (has function op some effector T cell function c))
has super-classes
cultured immune cell population c

cultured immune cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001875

a cultured cell population comprised of a single type of immune system cell
Source
PERSON:Matthew Brush
has super-classes
cultured cell population c
has sub-classes
cultured CD3+ T cell population c, cultured CD3- T cell population c, cultured CD4- T cell population c, cultured CD8- T cell population c, cultured PBMC cell population c, cultured antigen presenting cell population c, cultured effector T cell population c

cultured PBMC cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110044

A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types).
Source
IEDB
is equivalent to
cultured immune cell population c and (is_specified_output_of op some isolation of PBMCs c)
has super-classes
cultured immune cell population c

curated informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302840

A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.
Source
OBI
Example
PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6.
has super-classes
information content entity c
is_specified_output_of op some digital curation c

curation status specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000078

The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Source
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
is equivalent to
{ example to be eventually removed , metadata complete , organizational term , ready for release , metadata incomplete , uncurated , pending final vetting , to be replaced with external ontology term , requires discussion }
has super-classes
data about an ontology part c
has members
example to be eventually removed ni, requires discussion ni, to be replaced with external ontology term ni

current amplification functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001040

A current amplification function is an amplification function that increases the amplitude of a current.
has super-classes
function c

curve fitting data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200072

A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints.
Source
WEB: http://en.wikipedia.org/wiki/Curve_fitting
is equivalent to
(has_specified_output op some data set of predicted values according to fitted curve c) or (achieves_planned_objective op some curve fitting objective c)
has super-classes
data transformation c
has sub-classes
biexponential transformation c, loess fitting c, log-log curve fitting c, logistic-log curve fitting c, logit-log curve fitting c

curve fitting objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200174

A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
Source
PERSON: Elisabetta Manduchi
has super-classes
data transformation objective c

custom made columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000621

A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234
has super-classes
chromatography column c

Cy3 dyec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_37987

has super-classes
molecular label c
has role op some molecular label role c

Cy5 dyec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_37989

has super-classes
molecular label c
has role op some molecular label role c

Cyanc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400022

A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells.
Source
http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm
has super-classes
flow cytometer analyzer c

CYFlow MLc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400023

A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting.
Source
http://www.partec.de/products/cyflow-ml.html
has super-classes
flow cytometer analyzer c

CyFlow SLc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400024

a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels.
Source
http://www.partec.de/products/cyflow.html
has super-classes
flow cytometer analyzer c

CyFlow SL3c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400025

A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement.
Source
http://www.partec.de/products/cyflowsl3.html
has super-classes
flow cytometer analyzer c

CyFlow Spacec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400026

A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research.
Source
http://www.partec.de/products/cyflowspace.html
Example
CyFlow Space at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

CytoBuoy flow cytometer analyzerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400027

A flow cytometer analyser which is manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters.
Source
http://www.cytobuoy.com/
Example
CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations
has super-classes
flow cytometer analyzer c
is_manufactured_by op value CytoBuoy

cytochalasinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_23528

has super-classes
molecular entity c

cytochalasin-induced inhibition of actin polymerization assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001689

is an assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041).
is equivalent to
(assay c and (has_specified_input op some cytochalasin c) and (has_specified_output op some data item c and (is about op some actin filament polymerization c))) and (achieves_planned_objective op some biological feature identification objective c)
has super-classes
assay c

cytokine productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0001816

The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
biological_process c
has sub-classes
Oncostatin M production c, TRAIL production c, chemokine production c, connective tissue growth factor production c, cytokine production involved in immune response c, cytokine production involved in inflammatory response c, epitope specific cytokine production by T cells c, granulocyte colony-stimulating factor production c, granulocyte macrophage colony-stimulating factor production c, hepatocyte growth factor production c, interferon-beta production c, interferon-gamma production c, interleukin-1 production c, interleukin-10 production c, interleukin-11 production c, interleukin-12 production c, interleukin-13 production c, interleukin-14 production c, interleukin-15 production c, interleukin-16 production c, interleukin-17 production c, interleukin-18 production c, interleukin-19 production c, interleukin-2 production c, interleukin-20 production c, interleukin-21 production c, interleukin-22 production c, interleukin-23 production c, interleukin-24 production c, interleukin-25 production c, interleukin-26 production c, interleukin-27 production c, interleukin-3 production c, interleukin-4 production c, interleukin-5 production c, interleukin-6 production c, interleukin-7 production c, interleukin-8 production c, interleukin-9 production c, macrophage migration inhibitory factor production c, platelet activating factor production c, transforming growth factor beta production c, transforming growth factor beta1 production c, transforming growth factor beta2 production c, transforming growth factor beta3 production c, tumor necrosis factor superfamily cytokine production c, type I interferon production c, type III interferon production c, vascular endothelial growth factor production c

cytokine production involved in immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0002367

The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

cytokine production involved in inflammatory responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0002534

The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

cytological stain rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000026

A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization
Example
haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin
has super-classes
dye role c

cytometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400137

A cytometer is an instrument for counting and measuring cells.
Source
http://medical.merriam-webster.com/medical/cytometer
has super-classes
measurement device c
(has part op some light source c) and (has part op some optical filter c) and (has part op some photodetector c)
has function op some measure function c
has sub-classes
flow cytometer c

cytometer sample tubec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400091

A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
sample tube in a cytometer
has super-classes
test tube c

cytometric bead array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000920

An analyte assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes.
Source
IEDB
Example
Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture.
is equivalent to
analyte assay c and ((realizes op some reagent role c and (inheres in op some assay bead c)) and (has_specified_input op some assay bead c)) and (has part op some fluorescence detection assay c)
has super-classes
analyte assay c

cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001828

An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c

cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002061

An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells c

cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001764

An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c

cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001754

An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c

cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001397

An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c

cytometric bead array assay measuring epitope specific granzyme A release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002063

A T cell epitope specific granzyme A release assay that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granzyme A release by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific granzyme A release by T cells c

cytometric bead array assay measuring epitope specific granzyme B release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002065

A T cell epitope specific granzyme B release assay that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granzyme B release by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific granzyme B release by T cells c

cytometric bead array assay measuring epitope specific interferon-gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001379

An assay of epitope specific interferon-gamma production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-gamma production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interferon-gamma production by T cells c

cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001747

An assay of epitope specific interleukin-1 alpha production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c

cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001223

An assay of epitope specific interleukin-1 beta production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c

cytometric bead array assay measuring epitope specific interleukin-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001297

An assay of epitope specific interleukin-10 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-10 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-10 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001284

An assay of epitope specific interleukin-12 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-12 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-12 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001349

An assay of epitope specific interleukin-13 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-13 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-13 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-17 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001296

An assay of epitope specific interleukin-17 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-17 production by T cells c
has sub-classes
cytometric bead array assay measuring epitope specific interleukin-17A production by T cells c, cytometric bead array assay measuring epitope specific interleukin-17F production by T cells c

cytometric bead array assay measuring epitope specific interleukin-17A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001512

A T cell epitope specific interleukin-17A production assay that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17A production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
cytometric bead array assay measuring epitope specific interleukin-17 production by T cells c
biological activity assay measuring epitope specific interleukin-17A production by T cells c

cytometric bead array assay measuring epitope specific interleukin-17F production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001523

A T cell epitope specific interleukin-17F production assay that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17F production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
cytometric bead array assay measuring epitope specific interleukin-17 production by T cells c
biological activity assay measuring epitope specific interleukin-17F production by T cells c

cytometric bead array assay measuring epitope specific interleukin-18 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001835

An assay of epitope specific interleukin-18 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-18 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-18 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-2 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001300

An assay of epitope specific interleukin-2 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-2 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-2 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-27 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001811

An assay of epitope specific interleukin-27 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-27 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-27 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-3 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001807

An assay of epitope specific interleukin-3 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-3 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-3 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001326

An assay of epitope specific interleukin-4 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-4 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-4 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-5 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001289

An assay of epitope specific interleukin-5 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-5 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-5 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-6 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001360

An assay of epitope specific interleukin-6 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-6 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-6 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-7 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001585

An assay of epitope specific interleukin-7 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-7 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-7 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-8 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001457

An assay of epitope specific interleukin-8 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-8 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-8 production by T cells c

cytometric bead array assay measuring epitope specific interleukin-9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001532

An assay of epitope specific interleukin-9 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring interleukin-9 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring interleukin-9 production by T cells c

cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001601

An assay of epitope specific interleukin-21 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-21 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-21 production by T cells c

cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001577

An assay of epitope specific interleukin-22 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-22 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-22 production by T cells c

cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001610

An assay of epitope specific interleukin-23 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-23 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-23 production by T cells c

cytometric bead array assay measuring epitope specific IP-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001196

An assay of epitope specific IP-10 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific IP-10 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific IP-10 production by T cells c

cytometric bead array assay measuring epitope specific lymphotoxin A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001793

An assay of epitope specific lymphotoxin A production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific lymphotoxin A production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific lymphotoxin A production by T cells c
cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c

cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001405

An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c

cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001781

An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c

cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002067

An assay of epitope specific macrophage migration inhibitory factor (MIF) production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells c

cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001243

An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c

cytometric bead array assay measuring epitope specific oncostatin M production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002068

An assay of epitope specific oncostatin M production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific oncostatin M production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific oncostatin M production by T cells c

cytometric bead array assay measuring epitope specific RANTES production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001412

An assay of epitope specific RANTES production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific RANTES production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific RANTES production by T cells c

cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001210

An assay of epitope specific transforming growth factor-beta production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c

cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001353

A T cell epitope specific tumor necrosis factor production assay that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c

cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001368

An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
has sub-classes
cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells c, cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells c

cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001787

An assay of epitope specific vascular endothelial growth factor production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c

cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001490

An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cytometric bead array assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c and (has part op some cytometric bead array assay c)
has super-classes
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c

cytometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001977

An assay that measures properties of cells.
Source
IEDB
Example
An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.
is equivalent to
assay c and ((realizes op some evaluant role c and (inheres in op some cell c)) and (has_specified_input op some cell c))
has super-classes
assay c
has sub-classes
cell proliferation assay c, cell-cell binding detection by flow cytometry assay c, cell-cell killing assay c, cytometry time of flight assay c, enzyme-linked immunospot assay c, flow cytometry assay c, mixed lymphocyte reaction assay c

cytometry time of flight assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002115

A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry.
Source
http://www.ncbi.nlm.nih.gov/pubmed/26190063
Example
Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining refelctive of the level of expression of those surface receptors.
has super-classes
cytometry assay c
(realizes op some molecular label role c and (inheres in op some rare earth metal atom c)) and (has_specified_input op some rare earth metal atom c)
has part op some mass spectrometry assay c

cytoplasmic RNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000876

A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
Source
UPenn Group
Example
Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
has super-classes
RNA extract c
is_specified_output_of op some cytoplasmic RNA extraction c

cytoplasmic RNA extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000859

A RNA extraction process in which the desired output material is RNA in the cytoplasm.
Source
UPenn Group
has super-classes
RNA extraction c

CytoSencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400028

A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites.
Source
http://www.cytobuoy.com/
has super-classes
flow cytometer analyzer c

CytoSubc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400029

A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle.
Source
http://www.cytobuoy.com/
has super-classes
flow cytometer analyzer c

cytotoxic T cell degranulationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0043316

The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell.
has super-classes
cell killing c
has sub-classes
epitope specific cytotoxic T cell degranulation c

damagedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001167

A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired.
has super-classes
quality of a single physical entity c

Danio rerioc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_7955

has super-classes
Euteleostomi c

Daphniac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_6668

has super-classes
Pancrustacea c

data about an ontology partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000102

data about an ontology part is a data item about a part of an ontology, for example a term
has super-classes
data item c
has sub-classes
curation status specification c, db xref c, definition c, denotator type c, obsolescence reason specification c, subset c, synonym c, synonym type c

data analysis servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001529

A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output.
Source
PERSON: Matthew Brush
Example
Statistaical analysis service, data visualization service
has super-classes
data service c
has part op some data transformation c

data combinationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200125

A data transformation in which individual input data elements and values are merged together into a output set of data elements and values.
Source
editor
has super-classes
data transformation c
achieves_planned_objective op some merging objective c

data encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000227

a documenting process to encode an information entity into a digital document
Source
OBI branch derived
Example
storage of measurement results from an assay into a text file, such as
has super-classes
documenting c

data format specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000098

A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
Source
OBI branch derived
OBI_0000187
has super-classes
directive information entity c
has members
ACS ni, Compensation-ML ni, FCS ni, Gating-ML ni, OWL ni, RDF ni, Transformation-ML ni, XML ni, tar ni, zip ni

data imputationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200061

Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm.
Source
ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60.
has super-classes
data transformation c

data itemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000027

a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
Example
Data items include counts of things, analyte concentrations, and statistical summaries.
has super-classes
information content entity c
has sub-classes
average value c, binding datum c, cartesian spatial coordinate datum c, center value c, data about an ontology part c, data set c, genetic characteristics information c, genome coverage c, measurement datum c, number of errors c, operational taxonomic unit matrix c, predicted data item c, quantitative confidence value c, setting datum c
is in range of
is_supported_by_data op

data item extraction from journal articlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000443

a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
has super-classes
planned process c
has_specified_input op some journal article c
has_specified_output op some data item c

data maintenance servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001598

A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance.
Source
PERSON: Matthew Brush
Example
A database management service, a web hosting service.
has super-classes
data service c

data normalization objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200167

A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
Source
PERSON: James Malone
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
Example
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
has super-classes
data transformation objective c

data partitioningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200156

Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets.
Source
PERSON: Melanie Courtot
PERSON: Richard Scheuermann
PERSON: Ryan Brinkman
has super-classes
data transformation c

data representational modelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000658

Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
Source
GROUP: OBI
Example
gene regulatory graph model
phylogenetic tree
protein interaction network
has super-classes
directive information entity c

data servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001530

A service that has some information content entity as input and output.
Information content entity was used as specified input and output since it was more appropriate then data item or dataset.
Source
PERSON: Carlo Torniai
Example
Data analysis service such statistical abalysis or storage service such data backup.
has super-classes
service c
has_specified_input op some information content entity c
has_specified_output op some information content entity c
has sub-classes
data analysis service c, data maintenance service c, data storage service c

data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000100

A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
Source
OBI_0000042
group:OBI
Example
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has super-classes
data item c
has sub-classes
background corrected data set c, centrally registered identifier registry c, classified data set c, cluster c, clustered data set c, data set of features c, data set of predicted values according to fitted curve c, error corrected data set c, gene list c, normalized data set c, reduced dimension data set c, time sampled measurement data set c

data set of featuresc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000649

A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
is equivalent to
is_specified_output_of op some descriptive statistical calculation data transformation c
has super-classes
data set c

data set of predicted values according to fitted curvec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000656

A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints.
is equivalent to
is_specified_output_of op some curve fitting data transformation c
has super-classes
data set c

data storage servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001533

A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form.
Source
PERSON: Matthew Brush
Example
A service offering data backup
has super-classes
data service c

data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200000

A planned process that produces output data from input data.
Source
Branch editors
Example
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
is equivalent to
achieves_planned_objective op some data transformation objective c
has super-classes
planned process c
realizes op some concretizes op some algorithm c and (has part op some objective specification c)
has_specified_input op some data item c
has_specified_output op some data item c
has_specified_input op only data item c
has_specified_output op only data item c
has sub-classes
ANOVA c, Likelihood-ratio test c, MA transformation c, averaging data transformation c, background correction data transformation c, center calculation data transformation c, class discovery data transformation c, class prediction data transformation c, curve fitting data transformation c, data combination c, data imputation c, data partitioning c, decision tree building data transformation c, descriptive statistical calculation data transformation c, differential expression analysis data transformation c, discriminant analysis c, error correction data transformation c, feature extraction c, longitudinal data analysis c, mass spectrometry analysis c, mathematical feature c, network analysis c, non-negative matrix factorization c, normalization data transformation c, partitioning data transformation c, peak matching c, performing a diagnosis c, polynomial transformation c, probabilistic algorithm c, regression analysis method c, scaling data transformation c, sequence analysis data transformation c, sequence assembly process c, split-scale transformation c, spread calculation data transformation c, statistical hypothesis test c, survival analysis data transformation c
is disjoint with
assay c, information acquisition c

data transformation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200166

An objective specification to transformation input data into output data
Source
PERSON: James Malone
Example
normalize objective
has super-classes
objective specification c
has sub-classes
averaging objective c, center calculation objective c, class discovery objective c, class prediction objective c, correction objective c, correlation study objective c, curve fitting objective c, data normalization objective c, data vector reduction objective c, decision tree induction objective c, descriptive statistical calculation objective c, differential expression analysis objective c, feature extraction objective c, fuzzy clustering objective c, inter-rater reliability objective c, merging objective c, partitioning objective c, pattern matching objective c, scaling objective c, sequence analysis objective c, spectrum analysis objective c, spread calculation objective c, statistical hypothesis test objective c, survival analysis objective c

data vector reduction data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200182

A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k.
Source
PERSON: James Malone
is equivalent to
(has_specified_output op some reduced dimension data set c) or (achieves_planned_objective op some data vector reduction objective c)
has super-classes
decision tree building data transformation c
has sub-classes
gating c

data vector reduction objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200157

Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k.
Source
PERSON: Richard H. Scheuermann
has super-classes
data transformation objective c

data visualizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200111

An planned process that creates images, diagrams or animations from the input data.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
PERSON: Tina Boussard
Example
Generation of a heatmap from a microarray dataset
has super-classes
planned process c
has_specified_input op some data item c
has_specified_output op some graph c or image c
has_specified_input op only data item c
has_specified_output op only graph c or image c
has sub-classes
background corrected data visualization c, classified data visualization c, clustered data visualization c, gene list visualization c

datum labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000009

A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
has super-classes
information content entity c
has sub-classes
categorical label c, measurement unit label c

db xrefc back to ToC or Class ToC

IRI: http://www.geneontology.org/formats/oboInOwl#DbXref

has super-classes
data about an ontology part c

deadc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001422

A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
has super-classes
quality of a single physical entity c

decapitated organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302837

decapitated organism is an organism which has had it's head removed
Source
OBI Biomaterial
Example
Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172
is equivalent to
material entity c and (is_specified_output_of op some decapitation c)
has super-classes
processed material c

decapitationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302899

decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..)
Source
OBI-Branch
Example
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
has super-classes
animal euthanization c

decision analysis study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001965

a study design that has a decision analysis objective specification as part
Source
PERSON: Bill Hogan
is equivalent to
study design c and (has part op some decision-theoretic analysis objective c)
has super-classes
study design c

decision tree building data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000707

A decision tree building data transformation is a data transformation that has objective decision tree induction.
Source
PERSON: James Malone
is equivalent to
achieves_planned_objective op some decision tree induction objective c
has super-classes
data transformation c
has sub-classes
CART c, data vector reduction data transformation c

decision tree induction objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000704

A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
has super-classes
data transformation objective c

decision-theoretic analysis objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001964

An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric.
Source
PERSON: Bill Hogan
has super-classes
objective specification c

definitionc back to ToC or Class ToC

IRI: http://www.geneontology.org/formats/oboInOwl#Definition

has super-classes
data about an ontology part c

denatured polymerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302835

Is a polymer which has lost secondary or tertiary structure
Source
http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29
is equivalent to
macromolecule c and (is_specified_output_of op some denaturing c)
has super-classes
macromolecule c
processed material c

denaturingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000803

Is a process in which the tertiary or secondary structure of a polymer is disrupted
Source
http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29
Example
Denaturing DNA in alcohol
has super-classes
material processing c
has_specified_input op some nucleic acid c or protein c
achieves_planned_objective op some material transformation objective c

denaturing high-performance liquid chromatography instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001133

A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis.
Source
doi:10.1385/1-59259-850-1:173
has super-classes
material separation device c
has function op some material separation function c

dendritic cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000451

A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
has super-classes
cell c

dendrogramc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000183

A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
Source
WEB: http://en.wikipedia.org/wiki/Dendrogram
Example
Dendrograms are often used in computational biology to illustrate the clustering of genes.
has super-classes
graph c

denotator typec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000409

A denotator type indicates how a term should be interpreted from an ontological perspective.
Source
Barry Smith, Werner Ceusters
Example
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
is equivalent to
{ universal , defined class , named class expression }
has super-classes
data about an ontology part c
has members
defined class ni, named class expression ni, universal ni

densitometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001062

A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface.
Source
http://en.wikipedia.org/wiki/Densitometer
has super-classes
measurement device c
has function op some measure function c

density plotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000079

A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
Source
OBI_0000179
group:Flow Cytometry community
Example
Density plot of SSC-H and FSC-H.
has super-classes
graph c

deoxyribonuclease-1c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000006592

A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof.
has super-classes
protein c

deoxyribonucleic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16991

High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
has super-classes
nucleic acid c
has sub-classes
amplified DNA c, double-stranded DNA c, forward PCR primer c, multiplexing sequence identifier c, reverse PCR primer c

DEPC structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000897

is a single-nucleotide-resolution nucleic acid structure mapping assay which uses DEPC as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28.
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some diethyl pyrocarbonate c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

dermisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002067

The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
has super-classes
material anatomical entity c

descriptive statistical calculation data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200184

A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
Source
PERSON: James Malone
is equivalent to
(has_specified_output op some data set of features c) or (achieves_planned_objective op some descriptive statistical calculation objective c)
has super-classes
data transformation c
has sub-classes
arithmetic mean calculation c, geometric mean calculation c, interquartile-range calculation c, kurtosis calculation c, median calculation c, mode calculation c, quantile calculation c, skewness calculation c, standard deviation calculation c, variance calculation c

descriptive statistical calculation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200078

A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
PERSON: Monnie McGee
has super-classes
data transformation objective c

detection of molecular labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600017

an assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached
Source
OBI developer call, 3-12-12
Example
Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present
has super-classes
assay c
realizes op some molecular label role c
has_specified_input op some molecular-labeled material c
has_specified_output op some measurement datum c and (is about op some molecular-labeled material c)
achieves_planned_objective op some assay objective c
has sub-classes
carboxyfluorescein succinimidyl ester staining assay c, immuno staining assay c

detection of specific nucleic acid polymers with complementary probesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000874

An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes.
Source
IEDB
Example
Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays.
is equivalent to
analyte assay c and ((realizes op some reagent role c and (inheres in op some nucleic acid c and (has role op some complementary nucleotide probe role c))) and (has_specified_input op some nucleic acid c and (has role op some complementary nucleotide probe role c))) and ((realizes op some analyte role c and (inheres in op some nucleic acid c)) and (has_specified_input op some nucleic acid c))
has super-classes
analyte assay c
has sub-classes
chromatin isolation by RNA purification sequencing assay c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001827

An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002060

An assay of epitope specific chemokine (C-C motif) ligand 17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001767

An assay of epitope specific chemokine (C-C motif) ligand 19 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001762

An assay of epitope specific chemokine (C-C motif) ligand 21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001763

An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001765

An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001759

An assay of epitope specific chemokine (C-X-C motif) ligand 12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001760

An assay of epitope specific chemokine (C-X-C motif) ligand 13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001761

An assay of epitope specific chemokine (C-X-C motif) ligand 16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001757

An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001752

An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001357

An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002064

A T cell epitope specific granzyme A release assay that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granzyme A release by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific granzyme A release by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002066

A T cell epitope specific granzyme B release assay that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granzyme B release by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific granzyme B release by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001356

An assay of epitope specific interferon-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-beta production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interferon-beta production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001350

An assay of epitope specific interferon-gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-gamma production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interferon-gamma production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001746

An assay of epitope specific interleukin-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001743

An assay of epitope specific interleukin-1 beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001367

An assay of epitope specific interleukin-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-10 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-10 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001268

An assay of epitope specific interleukin-12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-12 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-12 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001542

An assay of epitope specific interleukin-13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-13 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-13 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001836

An assay of epitope specific interleukin-16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-16 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-16 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001291

An assay of epitope specific interleukin-17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-17 production by T cells c
has sub-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001840

A T cell epitope specific interleukin-17A production assay that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17A production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells c
biological activity assay measuring epitope specific interleukin-17A production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001832

A T cell epitope specific interleukin-17F production assay that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17F production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells c
biological activity assay measuring epitope specific interleukin-17F production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001815

An assay of epitope specific interleukin-18 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-18 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-18 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001277

An assay of epitope specific interleukin-2 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-2 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-2 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001298

An assay of epitope specific interleukin-21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-21 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-21 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001279

An assay of epitope specific interleukin-22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-22 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-22 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001395

An assay of epitope specific interleukin-23 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-23 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-23 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001382

An assay of epitope specific interleukin-27 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-27 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-27 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001808

An assay of epitope specific interleukin-3 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-3 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-3 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001339

An assay of epitope specific interleukin-4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-4 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-4 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001255

An assay of epitope specific interleukin-5 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-5 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-5 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001389

An assay of epitope specific interleukin-6 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-6 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-6 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001676

An assay of epitope specific interleukin-7 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-7 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-7 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001801

An assay of epitope specific interleukin-8 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-8 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-8 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001799

An assay of epitope specific interleukin-9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring interleukin-9 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring interleukin-9 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001383

An assay of epitope specific IP-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific IP-10 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific IP-10 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001794

An assay of epitope specific lymphotoxin A production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific lymphotoxin A production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific lymphotoxin A production by T cells c
detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001792

An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001782

An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001343

An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin releasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001245

A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific perforin release by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific perforin release by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001325

An assay of epitope specific RANTES production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific RANTES production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific RANTES production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001203

An assay of epitope specific transforming growth factor-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001242

A T cell epitope specific tumor necrosis factor production assay that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c
detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001788

An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
has sub-classes
detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells c, detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells c

detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001766

An assay of epitope specific vascular endothelial growth factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c

detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001843

An assay of epitope specific interleukin-15 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-15 production by T cells c and (has part op some detection of specific nucleic acid polymers with complementary probes c)
has super-classes
biological activity assay measuring epitope specific interleukin-15 production by T cells c

detector lampc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000604

A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed.
Source
WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119
has super-classes
chromatography consumable c

detector reagent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000091

a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
Source
One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009
has super-classes
role c

deuterium atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_29237

The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second).
has super-classes
molecular entity c
atom c

devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000968

A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
Source
OBI development call 2012-12-17.
Example
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has super-classes
processed material c
is_specified_output_of op some material processing c
has function op some function c
has sub-classes
Bruker SampleRail system c, NMR console c, NMR magnet c, NMR sample holder c, NMR tube washing system c, PET synthesizer c, X-ray source c, analog-to-digital converter c, arrayer c, assay array c, automatic staining machine c, automatic tissue processor c, autosampler c, blot module c, capillary blotter c, cell harvester c, charge plate c, chip spotting device c, computer c, container c, cryofixation device c, digital-to-analog converter c, electrode puller c, environmental control device c, freeze substitution system c, ion source c, light emission device c, liquid handler c, lyophilizer c, magic angle spinning rotor c, material separation device c, measurement device c, microdissection instrument c, micromanipulator c, micropipette puller c, microplate washer c, microscope slide c, microtome knife maker c, microtome knife sharpener c, microwave synthesis system c, needle c, optical subsystem c, perfusion station c, perturbation device c, plate loader c, plate shaker c, power supply c, pump valve switch c, rocker c, spot cutter c, surface plasmon resonance sensor chip c, syringe c, tissue embedding station c, vacuum manifold c, vitrification apparatus c, voltage amplifier c

device creation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000996

an objective which aims to create a device with a specified function
Source
OBI
has super-classes
material transformation objective c

device settingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000654

a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
Example
Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
has super-classes
quality c
inheres in op some processed material c

diagnosis textual entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000075

diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
has super-classes
textual entity c

diagramc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000309

A figure that expresses one or more propositions
Example
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
has super-classes
figure c
has sub-classes
graph c

dialysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600052

a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
Source
OBI branch derived
Example
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c

dichroic filterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400030

A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
Source
http://en.wikipedia.org/wiki/Dichroic_filter
Example
Cy3 Dichroic Filter
has super-classes
optical filter c

dichroic mirrorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400031

A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
Source
http://en.wikipedia.org/wiki/Dichroic_mirror
Example
ViewLux Alexa 594 dichroic mirror
has super-classes
optical filter c

Dictyostelium discoideumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_44689

has super-classes
Eukaryota c

diethyl pyrocarbonatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_59051

The diethyl ester of dicarbonic acid.
has super-classes
molecular entity c

differential expression analysis data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000650

A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
Source
WEB:
is equivalent to
achieves_planned_objective op some differential expression analysis objective c
has super-classes
data transformation c

differential expression analysis objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200031

A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
Source
PERSON: Elisabetta Manduchi
Example
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
has super-classes
data transformation objective c

differential pressure gaugec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400032

Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
LSR2 differential pressure gauge
has super-classes
measurement device c
has function op some measure function c

diffractometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001122

A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it.
Source
http://en.wikipedia.org/wiki/Diffractometer
has super-classes
measurement device c
has function op some measure function c

digestive system fluid or secretionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0006911

has super-classes
organism substance c

digestive system fluid or secretion specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002504

A specimen that is derived from digestive system fluid or secretion.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some digestive system fluid or secretion c))
has super-classes
specimen from organism c

digital camerac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001048

An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
Source
http://en.wikipedia.org/wiki/Digital_camera
has super-classes
image creation device c
has function op some image acquisition function c

digital curationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302914

Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
Source
wikipedia
Example
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
has super-classes
documenting c

digital microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001126

A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor.
Source
http://en.wikipedia.org/wiki/Digital_microscope
has super-classes
microscope c
has function op some measure function c

digital object identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002110

A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles.
Source
https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/
Example
The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073
has super-classes
centrally registered identifier symbol c

digital-to-analog converterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400158

A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal.
Source
PERSON: Daniel Schober
Example
A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound.
has super-classes
device c
has function op some signal conversion function c

digoxigeninc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_42098

A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis.
has super-classes
molecular label c
has role op some molecular label role c

dilutedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001161

A concentration which relatively low.
has super-classes
quality of related physical entities c

dimensionality reductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200050

A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
has super-classes
class discovery data transformation c
(has_specified_output op some clustered data set c) and (achieves_planned_objective op some class discovery objective c)
has sub-classes
principal components analysis dimensionality reduction c, submatrix extraction c

dimethyl sulfatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_59050

The dimethyl ester of sulfuric acid.
has super-classes
molecular entity c

diode laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400033

A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer.
Source
John Quinn
Example
FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc.
has super-classes
laser c

diploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001394

A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father.
has super-classes
ploidy c

direct binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001591

a binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand.
Source
IEDB
Example
Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody.
has super-classes
binding assay c

direct detection NMR probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000491

An NMR probe designed to allow the direct detection of acquisition nuclei.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280
has super-classes
NMR probe c

direct submission to IEDBc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110300

A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB)
Source
IEDB
Example
The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB. The content of that report on the IEDB website is here: http://iedb.org/refId/1013357
has super-classes
report c

directed network graph constructionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200128

A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph.
Source
PERSON: Richard Scheuermann
has super-classes
network graph construction c

directive information entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000033

An information content entity whose concretizations indicate to their bearer how to realize them in a process.
has super-classes
information content entity c
is about op some realizable entity c
has sub-classes
action specification c, conditional specification c, data format specification c, data representational model c, dose specification c, objective specification c, plan specification c, selection criterion c, source code module c, study design controlled variable c, study design dependent variable c, study design independent variable c, target gene specification c, target subfragment specification c

DISCOVERY consolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000513

The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247
has super-classes
tecmag NMR console c

discriminant analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200106

Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
Source
WEB: http://www.statsoft.com/textbook/stdiscan.html
has super-classes
data transformation c
has sub-classes
canonical variate analysis c, discriminant function analysis c, linear discriminant functional analysis c, partial least square discriminant analysis c

discriminant function analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200099

Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
Source
WEB: http://www.statsoft.com/textbook/stdiscan.html
has super-classes
class prediction data transformation c
discriminant analysis c
class discovery data transformation c
(has_specified_output op some classified data set c) and (achieves_planned_objective op some class prediction objective c)
has_specified_output op some clustered data set c

discussion section of a publication about an investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000319

A part of a publication about an investigation that is about the study interpretation of the investigation
has super-classes
document part c

diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000031

A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
has super-classes
disposition c
has sub-classes
allergy c, autoimmune disease c, cancer c, infectious disease c

disease coursec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000063

The totality of all processes through which a given disease instance is realized.
is equivalent to
realizes op some disease c
has super-classes
biological_process c
has sub-classes
occurrence of allergy c, occurrence of infectious disease c

disease exacerbation in vivo intervention experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001981

An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host.
Source
IEDB
Example
Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide.
has super-classes
in vivo intervention experiment c

disease stagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000278

a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
Example
Stage II breast cancer, The timepoint of recovery from a disease
has super-classes
biological_process c
part of op some disease course c

disease state designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001293

A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
Source
MO_902 disease_state_design
has super-classes
study design c
has part op some organism feature identification objective c
has part op some study design independent variable c and (is about op some disease c)

display functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000400

A display function is a function to present information by translating that information through some lookup process into visual form.
has super-classes
information processor function c

dispositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000016

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
has super-classes
realizable entity c
has sub-classes
Insulin resistance c, disease c, disposition to be a product of antigen processing and presentation c, disposition to be bound by an MHC protein complex c, disposition to be bound by an adaptive immune receptor c, disposition to cause an allergic reaction c, disposition to infect an organism c, fluorescence c, function c, human pathogenicity disposition c, radioactive c
is disjoint with
role c

disposition to be a product of antigen processing and presentationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001511

A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell.
Source
IEDB
Example
The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER.
has super-classes
disposition c
realized in op only antigen processing and presentation c

disposition to be bound by an adaptive immune receptorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110045

Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor.
Source
IEDB
has super-classes
disposition c
realized in op only epitope binding by adaptive immune receptor c

disposition to be bound by an MHC protein complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001486

Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex.
Source
IEDB
has super-classes
disposition c
realized in op only MHC protein complex binding to ligand c

disposition to cause an allergic reactionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110010

The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease.
Source
IEDB
has super-classes
disposition c
realized in op only allergic reaction c

disposition to infect an organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110093

Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
Source
IEDB
has super-classes
disposition c
realized in op only infection process c

dissectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001504

A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
Source
EFO_0003856 dissection
MO_374 dissect
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

dissolved material entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302876

A material entity that has been going through a process of being put into solution
Example
Salt molecules that have been mixed into water
is equivalent to
material entity c and scattered molecular aggregate c and (part of op some is_specified_output_of op some creating a mixture of molecules in solution c)
has super-classes
scattered molecular aggregate c

divisive hierarchical clusteringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200155

A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain.
Source
PERSON: Elisabetta Manduchi
has super-classes
hierarchical clustering c

DMS structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001015

a single-nucleotide-resolution nucleic acid structure mapping assay which uses DMS as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA Ontology
Example
PMID:6159633 and PMID:2446263
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some dimethyl sulfate c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

DNA cleavage, restriction analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600055

the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments
Source
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
Example
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
has super-classes
enzymatic cleavage c
has_specified_input op some ribonucleic acid c

DNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001051

The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
Source
Group: UPenn group
has super-classes
nucleic acid extract c
is_specified_output_of op some DNA extraction c
has grain op some deoxyribonucleic acid c
has sub-classes
high molecular weight DNA extract c

DNA extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000257

A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
Source
OBI branch derived
has super-classes
nucleic acid extraction c
has_specified_output op some deoxyribonucleic acid c

DNA extraction/purification instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001117

A device that is used to isolate and collect DNA for subsequent molecular analysis.
Source
http://en.wikipedia.org/wiki/DNA_extraction
has super-classes
nucleic acid extraction/purification instrument c

DNA ligasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000023089

A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof.
has super-classes
enzyme c
protein c
has function op some catalytic activity c

DNA methylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0006306

The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
has super-classes
biological_process c

DNA methylation profiling assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000634

an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
Source
OBI branch derived
Example
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979
is equivalent to
has_specified_output op some information content entity c and (is about op some regulation of DNA methylation c)
has super-classes
analyte assay c
epigenetic modification assay c
realizes op some analyte role c and (role of op some deoxyribonucleic acid c)
has_specified_input op some specimen c and (has part op some deoxyribonucleic acid c)
achieves_planned_objective op some epigenetic modification identification objective c
has sub-classes
DNA methylation profiling by array assay c, DNA methylation profiling by high throughput sequencing assay c, MeDIP-seq assay c, amplification of intermethylated sites (AIMS) assay c

DNA methylation profiling by array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001332

An assay in which the methylation state of DNA is determined and is compared between samples using array technology
Philippe Rocca-Serra
Source
EFO_0002759 methylation profiling by array
is equivalent to
DNA methylation profiling assay c and (has participant op some DNA microarray c)
has super-classes
DNA methylation profiling assay c

DNA methylation profiling by array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001278

A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
Source
GROUP: ArrayExpress production team
has super-classes
study design c
has part op some epigenetic modification identification objective c
is concretized as op some realized in op some (has part op some DNA methylation profiling by array assay c) and (has participant op some DNA microarray c)

DNA methylation profiling by ChIP-chip assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002014

A ChIP-chip assay that identifies sites of DNA methylation.
Source
Penn group
has super-classes
ChIP-chip assay c
epigenetic modification assay c
has_specified_output op some information content entity c and (is about op some DNA methylation c)
achieves_planned_objective op some epigenetic modification identification objective c

DNA methylation profiling by high throughput sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001266

An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology
Philippe Rocca-Serra
Source
EFO_0002761 methylation profiling by high throughput sequencing
is equivalent to
DNA methylation profiling assay c and (has participant op some DNA sequencer c)
has super-classes
DNA methylation profiling assay c
has sub-classes
bisulfite sequencing c, methylation-sensitive restriction enzyme sequencing assay c

DNA methylation profiling by high throughput sequencing designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001435

A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology.
Source
GROUP: ArrayExpress production team
has super-classes
study design c
has part op some epigenetic modification identification objective c
is concretized as op some realized in op some (has part op some DNA methylation profiling by high throughput sequencing assay c) and (has participant op some DNA sequencer c)

DNA microarrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400148

A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
Source
Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03
Example
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
has super-classes
microarray c
has sub-classes
SNP microarray c, tiling microarray c

DNA polymerase activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0034061

Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
has super-classes
catalytic activity c

DNA polymerase amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600049

DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input
Source
OBI branch derived
Example
The use of taq polymerase to amplify a DNA fragment during a PCR.
has super-classes
enzymatic amplification c
has_specified_input op some DNA polymerase complex c
has_specified_input op some ribonucleic acid c and (located in op some material entity c)

DNA polymerase complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0042575

A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
has super-classes
protein complex c
enzyme c
has function op some DNA polymerase activity c

DNA replicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0006260

The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
has super-classes
biological_process c

DNA replication identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001916

A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time.
Source
Group: Penn Group
has super-classes
molecular feature identification objective c

DNA replication timing by array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001915

An assay in which timing of DNA replication is quantified as a function of genome position using array technology.
Source
Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067]
Example
Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067]
has super-classes
assay c
has part op some immunoprecipitation c
has part op some library preparation c
has part op some multiplex ligation-mediated amplification c
realizes op some evaluant role c and (role of op some deoxyribonucleic acid c)
has_specified_input op some 5-bromo-2'-deoxyuridine c
has_specified_output op some measurement datum c and (is about op some DNA replication c)
achieves_planned_objective op some DNA replication identification objective c
has participant op some flow cytometer sorter c
has participant op some DNA microarray c

DNA replication timing by sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001920

An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing.
Source
Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280]
Example
Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280]
has super-classes
sequencing assay c
has part op some DNA sequencing c
has part op some immunoprecipitation c
realizes op some evaluant role c and (role of op some deoxyribonucleic acid c)
has_specified_input op some 5-bromo-2'-deoxyuridine c
has_specified_output op some DNA sequence data c
has_specified_output op some information content entity c and (is about op some DNA replication c)
achieves_planned_objective op some DNA replication identification objective c
has participant op some flow cytometer sorter c
has participant op some DNA sequencer c

DNA residue methylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000831

a quality of a DNA residue that has a methyl group attached to it
has super-classes
quality of a single physical entity c

DNA sequence datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001573

A sequence data item that is about the primary structure of DNA
Source
OBI call; Melanie Courtout
Example
The part of a FASTA file that contains the letters ACTGGGAA
has super-classes
sequence data c
is about op some primary structure of DNA macromolecule c

DNA sequence feature detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000433

An assay with the objective to determine a sequence feature of DNA
Source
OBI
Example
genotyping using an Affymetrix chip
has super-classes
assay c
has_specified_input op some deoxyribonucleic acid c
has_specified_output op some measurement datum c
achieves_planned_objective op some sequence feature identification objective c
achieves_planned_objective op some assay objective c

DNA sequence variation detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000438

DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule.
Source
OBI Biomaterial
Example
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
has super-classes
assay c
has_specified_input op some deoxyribonucleic acid c
has_specified_output op some measurement datum c
achieves_planned_objective op some sequence feature identification objective c
achieves_planned_objective op some assay objective c

DNA sequencerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400103

A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Source
MO
Example
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
has super-classes
measurement device c
has function op some measure function c
has sub-classes
454 Genome Sequence 20 c, 454 Genome Sequencer FLX c, AB SOLiD System c, ABI 377 automated sequencer c, HeliScope Single Molecule Sequencer c, Illumina Genome Analyzer II c, Illumina HiSeq 1000 c, Illumina HiSeq 2000 c, Illumina HiSeq 2500 c, Illumina HiSeq 3000 c, Illumina HiSeq 4000 c, Li-Cor 4300 DNA Analysis System c, MiSeq c, NextSeq 500 c, PacBio RS II c

DNA sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000626

DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
Source
OBI Branch derived
Example
Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
is equivalent to
(has_specified_input op some deoxyribonucleic acid c and (has role op some evaluant role c)) and (has_specified_output op some DNA sequence data c)
has super-classes
sequencing assay c
achieves_planned_objective op some assay objective c
has participant op some DNA sequencer c
has sub-classes
DNA sequencing by ligation c, DNA sequencing by synthesis c, DNase I hypersensitive sites sequencing assay c, bisulfite sequencing c, exome sequencing assay c, formaldehyde-assisted isolation of regulatory elements assay c, methylation-sensitive restriction enzyme sequencing assay c, structural analysis by paired-end tag sequencing c, whole genome sequencing assay c

DNA sequencing by ligationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000723

is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step.
Example
PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22.
has super-classes
DNA sequencing c
has_specified_input op some DNA ligase c
has sub-classes
SOLiD sequencing c

DNA sequencing by synthesisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000734

is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
Example
PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25.
has super-classes
DNA sequencing c
has_specified_input op some DNA polymerase complex c
has sub-classes
Helicos sequencing c, Solexa sequencing c, chain termination sequencing c, pyrosequencing c

DNA sequencing servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000992

A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
has super-classes
sequencing service c
realizes op some service consumer role c
realizes op some service provider role c
provides_service_consumer_with op some DNA sequencing c

DNA Subtractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302906

a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library.
Source
OBI-Branch
Example
PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c

DNA synthesizerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001056

An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
Source
http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers
has super-classes
oligonucleotide synthesizer c

DNA transductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600059

a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism
Source
OBI branch derived
Example
The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein
has super-classes
genetic transformation c
has_specified_input op some Viruses c

DNA transfectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600060

a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell
Source
OBI branch derived
Example
The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest
has super-classes
transfection c
has_specified_input op some deoxyribonucleic acid c and (bearer of op some target of material addition role c)

DNASE 1 structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001016

a single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:3773731
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c
realizes op some catalytic activity c and (inheres in op some deoxyribonuclease-1 c)
has_specified_input op some deoxyribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

DNase I hypersensitive sites sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001853

An assay to identify the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I.
Source
http://en.wikipedia.org/wiki/DNase-Seq
Example
Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541]
has super-classes
DNA sequencing c
has part op some DNA sequencing c
has part op some library preparation c
has part op some non specific enzymatic cleavage c
has_specified_input op some deoxyribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some protein and DNA interaction identification objective c
has participant op some DNA sequencer c

documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000310

A collection of information content entities intended to be understood together as a whole
Example
A journal article, patent application, laboratory notebook, or a book
has super-classes
information content entity c
has sub-classes
edited document c, patent c, publication c, questionnaire c, report c

document editingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302908

is a planned process with specified input original document and specified output edited document
Source
adapted from wikipedia
Example
Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
has super-classes
planned process c
has_specified_input op some document c
has_specified_output op some edited document c

document partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000314

an information content entity that is part of a document
Example
An abstract, introduction, method or results section.
has super-classes
information content entity c
part of op some document c
has sub-classes
abstract c, acknowledgements section c, author contributions section c, author list c, copyright section c, discussion section of a publication about an investigation c, footnote c, institution list c, introduction to a publication about an investigation c, methods section c, references section c, results section c, supplementary material to a document c

document titlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000305

A textual entity that names a document
Example
Textual characteristics of traditional and Open Access scientific journals are similar
has super-classes
textual entity c
has sub-classes
running title c

documentingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000572

a planned process in which a document is created or added to by including the specified input in it.
Source
wikipedia http://en.wikipedia.org/wiki/Documenting
Example
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has super-classes
planned process c
has_specified_input op some information content entity c
has_specified_output op some document c
has sub-classes
data encoding c, digital curation c

donorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110087

A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
Source
IEDB
Example
A T cell line from a PPD(+) donor.
has super-classes
role c

dorsal toc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001233

A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity.
has super-classes
relational spatial quality c

dosec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000984

A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
Example
An organism has been injected 1ml of vaccine
has super-classes
measurement datum c

dose response curvec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001172

A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
has super-classes
line graph c

dose response designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001418

A study design that examines the relationship between the size of the administered dose and the extent of the response.
Source
MO_485 dose_response_design
has super-classes
compound treatment design c
has part op some biological feature identification objective c
has part op some study design independent variable c and (is about op some study intervention c and administration of material to specimen c)
has part op some study design independent variable c and (is about op some dose specification c and (is about op some administration of material to specimen c))

dose specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000969

a directive information entity that describes the dose that will be administered to a target
Example
a protocol specifying to administer 1 ml of vaccine to a mouse
has super-classes
directive information entity c

dot plotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000037

A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
Source
OBI_0000123
group:OBI
Example
Dot plot of SSC-H and FSC-H.
has super-classes
graph c

double blind study executionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000793

A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated
Source
http://clinicaltrials.gov/ct2/info/glossary#double
is equivalent to
treatment portion of study execution c and (has part op only not (informing investigator of subject study arm c or informing subject of study arm c))
has super-classes
single blind study execution c

double-stranded DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_4705

has super-classes
deoxyribonucleic acid c
has sub-classes
PCR product c, plasmid c, yeast artificial chromosome vector c

double-stranded RNA-specific adenosine deaminasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000003745

A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof.
has super-classes
protein c

drawing a conclusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001834

A planned process in which new information is inferred from existing information.
Example
Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting.
is equivalent to
has_specified_output op some conclusion textual entity c
has super-classes
planned process c
has_specified_input op some information content entity c
has sub-classes
comparative phenotypic assessment c

drawing a conclusion based on datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000338

A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
Source
Bjoern Peters
Example
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has super-classes
planned process c
has_specified_input op some data item c
has_specified_output op some conclusion based on data c
has sub-classes
assigning gene property based on phenotypic assessment c, comparative phenotypic assessment c, inductive reasoning c

droplet sorterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400153

A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal.
Source
OBI Instrument branch
has super-classes
material separation device c
has function op some sort function c

Drosophila melanogasterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_7227

has super-classes
Pancrustacea c

drug rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000040

a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism
Source
OBI, CDISC
Example
http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act.
has super-classes
role c
inheres in op some molecular entity c

dual loop autosamplerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000500

A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate).
Source
WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063
has super-classes
liquid chromatography autosampler c

Dulbecco's modified Eagle mediumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000918

A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins.
has super-classes
culture medium c
(has grain op some glucose c) and (has grain op some amino acid c)

dye laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400034

A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification.
Source
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
Rhodamine 101 dye laser used to irradiate cells in a flow cytometer.
has super-classes
laser c

dye rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000250

A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest.
Source
A substance used to color materials www.answers.com/topic/dye 19feb09
has super-classes
molecular label role c
has sub-classes
cytological stain role c, pH indicator dye role c, vital dye role c

dye swap designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500017

An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
Source
MO_858
Example
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
has super-classes
study design c

dye swap mergec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200055

A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
has super-classes
replicate analysis c

dye swap quality control rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001142

a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes
Source
MO_524 dye_swap_quality_control
has super-classes
reference substance role c
inheres in op some labeled nucleic acid extract c

Ecdysozoac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_1206794

has super-classes
Bilateria c
has sub-classes
Caenorhabditis elegans c, Pancrustacea c

edge betweenness calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200136

An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge.
Source
PERSON: Richard Scheuermann
has super-classes
edge quality calculation c

edge quality calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200135

A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network.
Source
PERSON: Richard Scheuermann
has super-classes
network analysis c
has sub-classes
edge betweenness calculation c

edge weightingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200070

Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network.
Source
editor
has super-classes
network analysis c

Edinburgh handedness assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001001

The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
Source
WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory
has super-classes
handedness assay c
has_specified_output op some Edinburgh score c
has_specified_input op value Edingburgh handedness inventory

Edinburgh scorec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000991

A score that measures the dominance of a person's right or left hand in everyday activities.
Source
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
has super-classes
scalar score from composite inputs c
is quality measurement of op some handedness c
is_specified_output_of op some Edinburgh handedness assay c
has measurement value dp min 1

edited documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302874

A document which is the output of a document editing process
Example
The OBI manuscript is (much) edited imformation
has super-classes
document c
is_specified_output_of op some document editing c

Edman degradationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000705

A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis.
Source
IEDB
Example
Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT.
has super-classes
sequencing assay c
(realizes op some molecular label role c and (inheres in op some material entity c)) and (has_specified_input op some material entity c)
has_specified_output op some information content entity c and (is about op some polypeptide c)

Edman degradation assay measuring MHC ligand processing and presentationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001509

A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands
Source
IEDB
is equivalent to
assay measuring MHC ligand processing and presentation c and (has part op some Edman degradation c)
has super-classes
assay measuring MHC ligand processing and presentation c

EDTA methidiumpropylamidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_59056

A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.
has super-classes
molecular entity c

effector T cell functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110084

The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex.
Source
IEDB
has super-classes
adaptive immune effector function c
inheres in op some T cell c
realized in op only adaptive immune response c and (process is result of op some MHC:epitope complex binding to TCR c)

efficacy of epitope intervention experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001178

An experiment that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism.
has super-classes
assay c
has part op some epitope specific immune intervention c
has_specified_output op some measurement datum c and (is about op some epitope c)
has sub-classes
epitope disease exacerbation experiment c, epitope protection experiment c, epitope tolerance induction experiment c, epitope treatment experiment c

eh transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200108

An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization.
Source
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Example
This type of transformation is typically used in flow cytometry.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

EL-4 cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110031

A cell line derived from mouse (C57BL/6N) lymphoma cells.
Source
IEDB
http://www.biotech.ist.unige.it/cldb/cl1160.html
has super-classes
immortal cell line c

electrical conductivity detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000565

The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area.
Source
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239
has super-classes
measurement device c
has function op some measure function c

electricity supply functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000384

An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
Example
the function of supplying current during a neuroscience experiment.
has super-classes
energy supply function c

electrocutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302895

electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process.
Source
OBI branch
Example
PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376.
has super-classes
animal euthanization c
has participant op some power supply c

electrode pullerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000955

A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube.
Source
http://faculty.plattsburgh.edu/donald.slish/Puller1.html
has super-classes
device c
has function op some mechanical function c

electron capture detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000509

The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes.
Source
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085
has super-classes
gas chromatography detector c

electron microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000990

A microscope that produces an image of an object by targeting it with an electron beam
has super-classes
microscope c

electron microscopy assay determining the 3D structure of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001646

A B cell epitope 3D structure determination assay that uses an electron microscopy imaging assay.
Source
IEDB
is equivalent to
3D structure determining assay of a 3D B cell epitope:antibody complex c and (has part op some electron microscopy imaging assay c) and (has_specified_output op some 3D structural organization datum c)
has super-classes
3D structure determining assay of a 3D B cell epitope:antibody complex c

electron microscopy assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001656

A B cell epitope qualitative binding to antibody assay that uses an electron microscopy imaging assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some electron microscopy imaging assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

electron microscopy imaging assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001631

An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material.
Source
IEDB
Example
Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure.
is equivalent to
imaging assay c and ((realizes op some function c and (inheres in op some electron microscope c)) and (has_specified_input op some electron microscope c))
has super-classes
microscopy assay c

electron paramagnetic resonance spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001102

An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion.
Source
http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance
has super-classes
spectrophotometer c

electronic case report formc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000167

An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11.
Source
CDISC glossary
has super-classes
information content entity c

electronic case report tabulationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000083

An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators.
Source
CDISC glossary
has super-classes
information content entity c

electronic repeater pipettec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001101

A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations.
Source
http://www.faqs.org/patents/app/20090196797
has super-classes
micropipette c

electrophoresisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600053

a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
Source
OBI branch derived
Example
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
has super-classes
material component separation c
has_specified_input op some polyacrylamide gel c or agarose gel c
achieves_planned_objective op some separation into different composition objective c
has participant op some gel tank c
has participant op some power supply c

electrophoresis systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001053

A device that moves charged particles through a medium by using an electric field induced by electrodes.
Source
http://en.wikipedia.org/wiki/Category:Electrophoresis
has super-classes
material separation device c
has function op some material separation function c
has sub-classes
agarose gel electrophoresis system c, capillary electrophoresis instrument c, gel electrophoresis system c

electrophoretic mobility shift assay c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001671

is an assay which aims to provide information about Protein-DNA or Protein-RNA interaction and which used gel electrophoresis and relies on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid.
Source
PMID:6269071
Example
Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. Puranik S, Kumar K, Srivastava PS, Prasad M. Plant Signal Behav. 2011 Oct;6(10):1588-90. Epub 2011 Oct 1. PMID: 21918373
is equivalent to
(assay c and (has_specified_input op some RNA extract c) and (has_specified_output op some data item c and (is about op some sequence-specific DNA binding c))) and (achieves_planned_objective op some assay objective c)
has super-classes
binding assay c

electroporationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302912

a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA
Source
WEB:http://en.wikipedia.org/wiki/Electroporation
Example
PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13.
has super-classes
cell permeabilization c
has_specified_input op some cell c
has participant op some power supply c

eligibility criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500026

an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
Source
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
Example
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
has super-classes
selection criterion c
has sub-classes
exclusion criterion c, inclusion criteria c

ELISA measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001657

A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunosorbent assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001315

An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c

ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001378

An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c

ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001330

An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c

ELISA measuring epitope specific granulocyte colony stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001521

An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c

ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110157

An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c

ELISA measuring epitope specific granulysin release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001663

A T cell epitope specific granulysin release assay that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulysin release by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific granulysin release by T cells c

ELISA measuring epitope specific granzyme B release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001461

A T cell epitope specific granzyme B release assay that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granzyme B release by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific granzyme B release by T cells c

ELISA measuring epitope specific interferon-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001751

An assay of epitope specific interferon-beta production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-beta production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interferon-beta production by T cells c

ELISA measuring epitope specific interferon-gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110151

An assay of epitope specific interferon-gamma production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-gamma production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interferon-gamma production by T cells c

ELISA measuring epitope specific interleukin-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001261

An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c

ELISA measuring epitope specific interleukin-1 beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110161

An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c

ELISA measuring epitope specific interleukin-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110156

An assay of epitope specific interleukin-10 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-10 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-10 production by T cells c

ELISA measuring epitope specific interleukin-12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110160

An assay of epitope specific interleukin-12 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-12 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-12 production by T cells c

ELISA measuring epitope specific interleukin-13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110159

An assay of epitope specific interleukin-13 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-13 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-13 production by T cells c

ELISA measuring epitope specific interleukin-15 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001283

An assay of epitope specific interleukin-15 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-15 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-15 production by T cells c

ELISA measuring epitope specific interleukin-16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001837

An assay of epitope specific interleukin-16 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-16 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-16 production by T cells c

ELISA measuring epitope specific interleukin-17 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110162

An assay of epitope specific interleukin-17 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-17 production by T cells c
has sub-classes
ELISA measuring epitope specific interleukin-17A production by T cells c, ELISA measuring epitope specific interleukin-17F production by T cells c

ELISA measuring epitope specific interleukin-17A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001675

A T cell epitope specific interleukin-17A production assay that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17A production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-17A production by T cells c
ELISA measuring epitope specific interleukin-17 production by T cells c

ELISA measuring epitope specific interleukin-17F production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001831

A T cell epitope specific interleukin-17F production assay that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17F production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-17F production by T cells c
ELISA measuring epitope specific interleukin-17 production by T cells c

ELISA measuring epitope specific interleukin-18 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110163

An assay of epitope specific interleukin-18 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-18 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-18 production by T cells c

ELISA measuring epitope specific interleukin-2 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110152

An assay of epitope specific interleukin-2 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-2 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-2 production by T cells c

ELISA measuring epitope specific interleukin-21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001346

An assay of epitope specific interleukin-21 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-21 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-21 production by T cells c

ELISA measuring epitope specific interleukin-22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001236

An assay of epitope specific interleukin-22 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-22 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-22 production by T cells c

ELISA measuring epitope specific interleukin-23 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001244

An assay of epitope specific interleukin-23 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-23 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-23 production by T cells c

ELISA measuring epitope specific interleukin-27 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001814

An assay of epitope specific interleukin-27 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-27 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-27 production by T cells c

ELISA measuring epitope specific interleukin-3 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001260

An assay of epitope specific interleukin-3 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-3 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-3 production by T cells c

ELISA measuring epitope specific interleukin-4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110153

An assay of epitope specific interleukin-4 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-4 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-4 production by T cells c

ELISA measuring epitope specific interleukin-5 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110154

An assay of epitope specific interleukin-5 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-5 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-5 production by T cells c

ELISA measuring epitope specific interleukin-6 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110158

An assay of epitope specific interleukin-6 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-6 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-6 production by T cells c

ELISA measuring epitope specific interleukin-7 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001803

An assay of epitope specific interleukin-7 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-7 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-7 production by T cells c

ELISA measuring epitope specific interleukin-8 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001359

An assay of epitope specific interleukin-8 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-8 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-8 production by T cells c

ELISA measuring epitope specific interleukin-9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001238

An assay of epitope specific interleukin-9 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring interleukin-9 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring interleukin-9 production by T cells c

ELISA measuring epitope specific IP-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001281

An assay of epitope specific IP-10 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific IP-10 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific IP-10 production by T cells c

ELISA measuring epitope specific lymphotoxin A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001288

An assay of epitope specific lymphotoxin A production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific lymphotoxin A production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
biological activity assay measuring epitope specific lymphotoxin A production by T cells c

ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001302

An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c

ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001438

An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c

ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001344

An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c

ELISA measuring epitope specific RANTES production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001222

An assay of epitope specific RANTES production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific RANTES production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific RANTES production by T cells c

ELISA measuring epitope specific transforming growth factor-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001231

An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c

ELISA measuring epitope specific tumor necrosis factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110155

A T cell epitope specific tumor necrosis factor production assay that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c

ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001246

An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
has sub-classes
ELISA measuring epitope specific lymphotoxin A production by T cells c, ELISA measuring epitope specific tumor necrosis factor production by T cells c

ELISA measuring epitope specific vascular endothelial growth factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001578

An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISA.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c and (has part op some enzyme-linked immunosorbent assay c)
has super-classes
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c

ELISA measuring the association constant [KA] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001735

A B cell epitope equilibrium association constant (KA) determination assay that uses an enzyme-linked immunosorbent assay.
Source
IEDB
is equivalent to
assay measuring the association constant [KA] of a B cell epitope:antibody complex c and (has part op some enzyme-linked immunosorbent assay c) and (has_specified_output op some has measurement unit label op value count per nanomolar)
has super-classes
assay measuring the association constant [KA] of a B cell epitope:antibody complex c

ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001728

A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an enzyme-linked immunosorbent assay.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c and (has part op some enzyme-linked immunosorbent assay c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c

ELISA microplate readerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001059

A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
Source
PERSON: Erik Segerdell
has super-classes
microplate reader c

ELISA microplate washerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001115

A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
Source
PERSON: Erik Segerdell
has super-classes
microplate washer c

ELISPOT assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001658

A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunospot assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some enzyme-linked immunospot assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001829

An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c

ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001758

An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c

ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001756

An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c

ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001753

An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c

ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001206

An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c

ELISPOT assay measuring epitope specific granzyme B release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001322

A T cell epitope specific granzyme B release assay that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granzyme B release by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific granzyme B release by T cells c

ELISPOT assay measuring epitope specific interferon-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001748

An assay of epitope specific interferon-beta production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-beta production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interferon-beta production by T cells c

ELISPOT assay measuring epitope specific interferon-gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110059

An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-gamma production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interferon-gamma production by T cells c

ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001745

An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c

ELISPOT assay measuring epitope specific interleukin-1 beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001842

An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c

ELISPOT assay measuring epitope specific interleukin-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110170

An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-10 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-10 production by T cells c

ELISPOT assay measuring epitope specific interleukin-12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001844

An assay of epitope specific interleukin-12 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-12 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-12 production by T cells c

ELISPOT assay measuring epitope specific interleukin-13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110171

An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-13 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-13 production by T cells c

ELISPOT assay measuring epitope specific interleukin-15 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001846

An assay of epitope specific interleukin-15 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-15 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-15 production by T cells c

ELISPOT assay measuring epitope specific interleukin-16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001838

An assay of epitope specific interleukin-16 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-16 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-16 production by T cells c

ELISPOT assay measuring epitope specific interleukin-17 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001354

An assay of epitope specific interleukin-17 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-17 production by T cells c
has sub-classes
ELISPOT assay measuring epitope specific interleukin-17A production by T cells c, ELISPOT assay measuring epitope specific interleukin-17F production by T cells c

ELISPOT assay measuring epitope specific interleukin-17A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001833

A T cell epitope specific interleukin-17A production assay that uses an ELISPOT.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17A production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
ELISPOT assay measuring epitope specific interleukin-17 production by T cells c
biological activity assay measuring epitope specific interleukin-17A production by T cells c

ELISPOT assay measuring epitope specific interleukin-17F production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001830

A T cell epitope specific interleukin-17F production assay that uses an ELISPOT.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17F production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
ELISPOT assay measuring epitope specific interleukin-17 production by T cells c
biological activity assay measuring epitope specific interleukin-17F production by T cells c

ELISPOT assay measuring epitope specific interleukin-18 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001817

An assay of epitope specific interleukin-18 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-18 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-18 production by T cells c

ELISPOT assay measuring epitope specific interleukin-2 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110013

An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-2 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-2 production by T cells c

ELISPOT assay measuring epitope specific interleukin-21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001826

An assay of epitope specific interleukin-21 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-21 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-21 production by T cells c

ELISPOT assay measuring epitope specific interleukin-22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001821

An assay of epitope specific interleukin-22 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-22 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-22 production by T cells c

ELISPOT assay measuring epitope specific interleukin-23 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001822

An assay of epitope specific interleukin-23 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-23 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-23 production by T cells c

ELISPOT assay measuring epitope specific interleukin-27 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001813

An assay of epitope specific interleukin-27 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-27 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-27 production by T cells c

ELISPOT assay measuring epitope specific interleukin-3 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001802

An assay of epitope specific interleukin-3 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-3 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-3 production by T cells c

ELISPOT assay measuring epitope specific interleukin-4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110167

An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-4 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-4 production by T cells c

ELISPOT assay measuring epitope specific interleukin-5 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001455

An assay of epitope specific interleukin-5 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-5 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-5 production by T cells c

ELISPOT assay measuring epitope specific interleukin-6 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001227

An assay of epitope specific interleukin-6 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-6 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-6 production by T cells c

ELISPOT assay measuring epitope specific interleukin-7 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001804

An assay of epitope specific interleukin-7 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-7 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-7 production by T cells c

ELISPOT assay measuring epitope specific interleukin-8 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001800

An assay of epitope specific interleukin-8 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-8 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-8 production by T cells c

ELISPOT assay measuring epitope specific interleukin-9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001797

An assay of epitope specific interleukin-9 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring interleukin-9 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring interleukin-9 production by T cells c

ELISPOT assay measuring epitope specific IP-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001795

An assay of epitope specific IP-10 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific IP-10 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific IP-10 production by T cells c

ELISPOT assay measuring epitope specific lymphotoxin A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001791

An assay of epitope specific lymphotoxin A production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific lymphotoxin A production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
biological activity assay measuring epitope specific lymphotoxin A production by T cells c

ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001780

An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c

ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001786

An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c

ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001784

An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c

ELISPOT assay measuring epitope specific perforin release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002069

A T cell epitope specific perforin release assay that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific perforin release by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific perforin release by T cells c

ELISPOT assay measuring epitope specific RANTES production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001790

An assay of epitope specific RANTES production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific RANTES production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific RANTES production by T cells c

ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001194

An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c

ELISPOT assay measuring epitope specific tumor necrosis factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110168

A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c

ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001272

An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
has sub-classes
ELISPOT assay measuring epitope specific lymphotoxin A production by T cells c, ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells c

ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001771

An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISPOT assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c and (has part op some enzyme-linked immunospot assay c)
has super-classes
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c

eluatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000318

a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
Source
OBI Bionaterial
Example
Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
has super-classes
processed material c
has part op some molecular entity c and (has role op some solvent role c)
is_specified_output_of op some elution c

elutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302905

the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
Source
wordnet.princeton.edu/perl/webwn
Example
PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13.
has super-classes
material processing c
has_specified_input op some molecular entity c and (has role op some solvent role c)
has_specified_output op some eluate c
achieves_planned_objective op some material transformation objective c
has participant op some chromatography column c

email addressc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000429

has super-classes
information content entity c
has sub-classes
email address of Bioinformatics Resource Center contact person c, email address of sequencing facility contact person c, email address of specimen collector c, email address of specimen provider principal investigator c

email address of Bioinformatics Resource Center contact personc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001887

An email address of the person who is contact representative of a Bioinformatics Resource Center
Source
NIAID GSCID-BRC metadata working group
is equivalent to
email address c and (is about op some Bioinformatics Resource Center contact person c)
has super-classes
email address c

email address of sequencing facility contact personc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001894

An email address of the contact representative at the sequencing facility
Source
NIAID GSCID-BRC metadata working group
is equivalent to
email address c and (is about op some sequencing facility contact person c)
has super-classes
email address c

email address of specimen collectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001890

An email address of the person collecting the specimen
Source
NIAID GSCID-BRC metadata working group
is equivalent to
email address c and (is about op some specimen collector c)
has super-classes
email address c

email address of specimen provider principal investigatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001903

An email address of the principal investigator providing the specimens for the investigation
Source
NIAID GSCID-BRC metadata working group
is equivalent to
email address c and (is about op some specimen provider principal investigator c)
has super-classes
email address c

eMedical recordc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000078

An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11.
Source
article-without-pmid-or-doi:CDISCglossary
has super-classes
information content entity c

energy supply functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000391

An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
has super-classes
function c
has sub-classes
electricity supply function c

enhanced cross-linking immunoprecipitation high-throughput sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002111

An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments.
Source
https://www.ncbi.nlm.nih.gov/pubmed/27018577
has super-classes
individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay c

enhancer activity detection by reporter gene assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002083

A reporter gene assay in which expression of a reporter gene is detected that was inserted under the control of an enhancer of interest.
Source
FaceBase, PMID 24614317
Example
PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules"
has super-classes
reporter gene assay c

entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000001

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
has super-classes
thing c
has sub-classes
continuant c, occurrent c
is disjoint with
Obsolete Class c

ENU structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001011

a single-nucleotide-resolution nucleic acid structure mapping assay which uses ENU as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:7002606 and PMID:2446263
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some N-ethyl-N-nitrosourea c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

environment control functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000401

An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
has super-classes
function c

environmental control devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001034

An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
Source
OBI
Example
A growth chamber is an environmental control device.
is equivalent to
has function op some heat function c or cool function c or environment control function c
has super-classes
device c
has sub-classes
autoclave c, cryostat c, heating block c, paraffin oven c, physical store c, slide warmer c, vacuum oven c

environmental exposure to infectious agentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110024

Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent
Source
IEDB
is equivalent to
biological_process c and (has participant op some organism c and ((has part op some infectious agent c) or (adjacent to op some infectious agent c)) and (has role op some host of immune response role c)) and (immediately preceded by op some environmental proximity to infectious agent c)
has super-classes
biological_process c

environmental history designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001226

A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
Source
MO_698 environmental_history_design
has super-classes
study design c
has part op some biological feature identification objective c

environmental materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_00010483

A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
has super-classes
material entity c

environmental material collection processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600012

environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
Source
IEDB
Example
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
has super-classes
specimen collection process c
has_specified_input op some environmental material c
has_specified_output op some specimen c
achieves_planned_objective op some specimen collection objective c

environmental proximity to infectious agentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110111

Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result
Source
IEDB
has super-classes
biological_process c
has sub-classes
contact to pathogen carrying biological vector c, living in endemic area c, living with infected household contact c, pathogen release in laboratory accident c

enzymatic amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600058

the use of enzymes to increase the number of molecules of a biomaterial
Source
OBI branch derived
Example
the use of a polymerase chain reaction to amplify a fragment of DNA
has super-classes
material processing c
realizes op some function c and (inheres in op some enzyme c)
has_specified_input op some material entity c and (has role op some nucleic acid template role c)
achieves_planned_objective op some material transformation objective c
has sub-classes
DNA polymerase amplification c, enzymatic DNA replication c, linear amplification c, polymerase chain reaction c, reverse transcribed polymerase chain reaction c

enzymatic cleavagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000231

enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme
Source
OBI branch derived
Example
Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
has super-classes
material processing c
realizes op some function c and (inheres in op some enzyme c)
has_specified_input op some specimen c
achieves_planned_objective op some material transformation objective c
has sub-classes
DNA cleavage, restriction analysis c, non specific enzymatic cleavage c, protease cleavage c, specific enzymatic cleavage c

enzymatic DNA replicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600057

the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial
Source
OBI branch derived
Example
the use of enzymes to duplicate DNA molecules
has super-classes
enzymatic amplification c

enzymatic ligationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302892

An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity
Source
OBI-Branch
Example
PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202.
has super-classes
material processing c
realizes op some function c and (inheres in op some enzyme c)
achieves_planned_objective op some material transformation objective c

enzymec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000427

(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
Source
GROUP:OBI
is equivalent to
material entity c and (ribonucleic acid c or protein complex c or protein c or (has part op some ribonucleic acid c) or (has part op some protein complex c) or (has part op some protein c)) and (has function op some catalytic activity c)
has super-classes
material entity c
has sub-classes
DNA ligase c, DNA polymerase complex c, restriction enzyme c, reverse transcriptase c

enzyme-linked antibodyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002047

A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added.
Source
OBI
Example
Goat anti-Mouse IgG-HRP (horse radish peroxidase) is an antibody linked to the enzyme horseradish peroxidase (HRP) that catalyzes the conversion of chromogenic substrates into colored products producing light when acting on chemiluminescent substrates (ECL).
has super-classes
processed material c
(has part op some immunoglobulin complex, circulating c) and (has part op some enzyme c)
is_specified_output_of op some addition of molecular label c

enzyme-linked immunosorbent assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000661

An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte.
Source
IEDB
Example
1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
has super-classes
analyte assay c
(realizes op some reagent role c and (inheres in op some immunoglobulin complex, circulating c)) and (has_specified_input op some immunoglobulin complex, circulating c)

enzyme-linked immunospot assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600031

A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest.
Source
IEDB
Example
Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell.
has super-classes
cytometry assay c
(realizes op some evaluant role c and (inheres in op some cultured cell population c)) and (has_specified_input op some cultured cell population c)
(realizes op some reagent role c and (inheres in op some immunoglobulin complex, circulating c)) and (has_specified_input op some immunoglobulin complex, circulating c)

epigenetic modification assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002020

An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation.
Source
Penn group
is equivalent to
assay c and (achieves_planned_objective op some epigenetic modification identification objective c)
has super-classes
assay c
has sub-classes
ChIP assay c, ChIP-seq assay c, DNA methylation profiling assay c, DNA methylation profiling by ChIP-chip assay c, histone modification identification by ChIP-chip assay c

epigenetic modification identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001234

A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Source
Person: Chris Stoeckert
has super-classes
molecular feature identification objective c

epithelial cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000066

A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
has super-classes
cell c
has sub-classes
hepatocyte c

epitheliumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000483

Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
has super-classes
tissue c

epitopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110001

a material entity bearing the epitope role
Source
IEDB
is equivalent to
bearer of op some disposition to be bound by an adaptive immune receptor c
has super-classes
material entity c

epitope binding by adaptive immune receptorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110014

is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding.
Source
IEDB
is equivalent to
realizes op some disposition to be bound by an adaptive immune receptor c and (inheres in op some material entity c and (bound_to op some adaptive immune receptor c))
has super-classes
biological_process c
has sub-classes
MHC:epitope complex binding to TCR c, immunoglobulin binding to epitope c

epitope disease exacerbation experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001188

an epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host.
has super-classes
efficacy of epitope intervention experiment c

epitope protection experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001184

an epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host.
has super-classes
efficacy of epitope intervention experiment c
has sub-classes
epitope protection experiment based on survival c, epitope protection from infectious challenge experiment c, epitope protection from tumor challenge experiment c

epitope protection experiment based on survivalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001189

an epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host.
has super-classes
epitope protection experiment c
has part op some survival assessment c

epitope protection from infectious challenge experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001179

An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed.
has super-classes
epitope protection experiment c
has part op some pathogen challenge c
has sub-classes
epitope protection from infectious challenge experiment based on pathogen burden c

epitope protection from infectious challenge experiment based on pathogen burden c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001186

An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls.
has super-classes
epitope protection from infectious challenge experiment c
has part op some infectious agent detection assay c

epitope protection from tumor challenge experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001183

An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed.
has super-classes
epitope protection experiment c

epitope specific chemokine (C-C motif) ligand 1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001219

A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-C motif) ligand 1 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-C motif) ligand 1 production c
epitope specific cytokine production by T cells c

epitope specific chemokine (C-C motif) ligand 19 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001825

A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-C motif) ligand 19 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-C motif) ligand 19 production c
epitope specific cytokine production by T cells c

epitope specific chemokine (C-C motif) ligand 21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001823

A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-C motif) ligand 21 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-C motif) ligand 21 production c
epitope specific cytokine production by T cells c

epitope specific chemokine (C-C motif) ligand 22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001819

A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-C motif) ligand 22 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-C motif) ligand 22 production c
epitope specific cytokine production by T cells c

epitope specific chemokine (C-C motif) ligand 4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001362

A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-C motif) ligand 4 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-C motif) ligand 4 production c
epitope specific cytokine production by T cells c

epitope specific chemokine (C-X-C motif) ligand 12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001818

A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-X-C motif) ligand 12 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-X-C motif) ligand 12 production c
epitope specific cytokine production by T cells c

epitope specific chemokine (C-X-C motif) ligand 13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001816

A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-X-C motif) ligand 13 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-X-C motif) ligand 13 production c
epitope specific cytokine production by T cells c

epitope specific chemokine (C-X-C motif) ligand 16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001820

A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-X-C motif) ligand 16 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-X-C motif) ligand 16 production c
epitope specific cytokine production by T cells c

epitope specific chemokine (C-X-C motif) ligand 9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001439

A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-X-C motif) ligand 9 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-X-C motif) ligand 9 production c
epitope specific cytokine production by T cells c

epitope specific cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001193

A process of cytokine production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
cytokine production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
cytokine production c
has sub-classes
epitope specific GM-CSF release by T cells c, epitope specific IFN-g release by T cells c, epitope specific IL-10 release by T cells c, epitope specific IL-12 release by T cells c, epitope specific IL-13 release by T cells c, epitope specific IL-17 release by T cells c, epitope specific IL-18 release by T cells c, epitope specific IL-1b release by T cells c, epitope specific IL-2 release by T cells c, epitope specific IL-4 release by T cells c, epitope specific IL-5 release by T cells c, epitope specific IL-6 release by T cells c, epitope specific IP-10 production by T cells c, epitope specific RANTES production by T cells c, epitope specific chemokine (C-C motif) ligand 1 production by T cells c, epitope specific chemokine (C-C motif) ligand 19 production by T cells c, epitope specific chemokine (C-C motif) ligand 21 production by T cells c, epitope specific chemokine (C-C motif) ligand 22 production by T cells c, epitope specific chemokine (C-C motif) ligand 4 production by T cells c, epitope specific chemokine (C-X-C motif) ligand 12 production by T cells c, epitope specific chemokine (C-X-C motif) ligand 13 production by T cells c, epitope specific chemokine (C-X-C motif) ligand 16 production by T cells c, epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c, epitope specific granulocyte colony stimulating factor production by T cells c, epitope specific interferon-beta production by T cells c, epitope specific interleukin-1 alpha production by T cells c, epitope specific interleukin-15 production by T cells c, epitope specific interleukin-16 production by T cells c, epitope specific interleukin-21 production by T cells c, epitope specific interleukin-22 production by T cells c, epitope specific interleukin-23 production by T cells c, epitope specific interleukin-27 production by T cells c, epitope specific interleukin-3 production by T cells c, epitope specific interleukin-7 production by T cells c, epitope specific interleukin-8 production by T cells c, epitope specific interleukin-9 production by T cells c, epitope specific macrophage inflammatory protein-1 alpha production by T cells c, epitope specific macrophage inflammatory protein-1 gamma production by T cells c, epitope specific monocyte chemotactic protein-1 production by T cells c, epitope specific transforming growth factor-beta production by T cells c, epitope specific tumor necrosis factor superfamily cytokine production by T cells c, epitope specific vascular endothelial growth factor production by T cells c

epitope specific cytotoxic T cell degranulationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001394

A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
cytotoxic T cell degranulation c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
cytotoxic T cell degranulation c

epitope specific GM-CSF release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110184

A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
granulocyte macrophage colony-stimulating factor production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
granulocyte macrophage colony-stimulating factor production c
epitope specific cytokine production by T cells c

epitope specific granulocyte colony stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001334

A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
granulocyte colony-stimulating factor production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
granulocyte colony-stimulating factor production c
epitope specific cytokine production by T cells c

epitope specific granulysin production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001677

A process of granulysin production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
granulysin production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
granulysin production c

epitope specific granzyme A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001678

A process of granzyme A production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
granzyme A production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
granzyme A production c

epitope specific granzyme B production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001371

A process of granzyme B production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
granzyme B production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
granzyme B production c

epitope specific helper T cell enhancement of T cell mediated immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001420

A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
helper T cell enhancement of T cell mediated immune response c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
helper T cell enhancement of T cell mediated immune response c

epitope specific IFN-g release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110185

A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interferon-gamma production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interferon-gamma production c
epitope specific cytokine production by T cells c

epitope specific IL-10 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110187

A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-10 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-10 production c
epitope specific cytokine production by T cells c

epitope specific IL-12 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110190

A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-12 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-12 production c
epitope specific cytokine production by T cells c

epitope specific IL-13 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110191

A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-13 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-13 production c
epitope specific cytokine production by T cells c

epitope specific IL-17 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110193

A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-17 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-17 production c
epitope specific cytokine production by T cells c
has sub-classes
epitope specific interleukin-17A production by T cells c, epitope specific interleukin-17F production by T cells c

epitope specific IL-18 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110195

A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-18 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-18 production c
epitope specific cytokine production by T cells c

epitope specific IL-1b release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110196

A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-1 beta production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-1 beta production c
epitope specific cytokine production by T cells c

epitope specific IL-2 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110056

A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-2 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-2 production c
epitope specific cytokine production by T cells c

epitope specific IL-4 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110199

A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-4 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-4 production c
epitope specific cytokine production by T cells c

epitope specific IL-5 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110202

A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-5 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-5 production c
epitope specific cytokine production by T cells c

epitope specific IL-6 release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110203

A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
interleukin-6 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-6 production c
epitope specific cytokine production by T cells c

epitope specific immune interventionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001192

An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope
has super-classes
passive immunization c
passive immunization c or Individual epitope immunization in vivo c
has sub-classes
B cell epitope specific immune intervention c, T cell epitope specific immune intervention c

epitope specific interferon-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001421

A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interferon-beta production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interferon-beta production c
epitope specific cytokine production by T cells c

epitope specific interleukin-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001257

A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-1 alpha production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-1 alpha production c
epitope specific cytokine production by T cells c

epitope specific interleukin-15 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001446

A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-15 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-15 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001275

A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-16 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-16 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-17A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001526

A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-17A production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-17A production c
epitope specific IL-17 release by T cells c

epitope specific interleukin-17F production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001470

A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-17F production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-17F production c
epitope specific IL-17 release by T cells c

epitope specific interleukin-21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001316

A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-21 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-21 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001399

A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-22 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-22 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-23 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001381

A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-23 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-23 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-27 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001262

A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-27 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-27 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-3 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001254

A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-3 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-3 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-7 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001535

A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-7 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-7 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-8 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001373

A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-8 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-8 production c
epitope specific cytokine production by T cells c

epitope specific interleukin-9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001415

A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
interleukin-9 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
interleukin-9 production c
epitope specific cytokine production by T cells c

epitope specific IP-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001462

A process of IP-10 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
IP-10 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
IP-10 production c
epitope specific cytokine production by T cells c

epitope specific killing by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110204

A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell.
Source
IEDB
is equivalent to
T cell mediated cytotoxicity c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
T cell mediated cytotoxicity c

epitope specific lymphotoxin A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001256

A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
lymphotoxin A production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
lymphotoxin A production c
epitope specific tumor necrosis factor superfamily cytokine production by T cells c

epitope specific macrophage inflammatory protein-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001207

A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
macrophage inflammatory protein-1 alpha production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
macrophage inflammatory protein-1 alpha production c
epitope specific cytokine production by T cells c

epitope specific macrophage inflammatory protein-1 gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001447

A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
macrophage inflammatory protein-1 gamma production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
macrophage inflammatory protein-1 gamma production c
epitope specific cytokine production by T cells c

epitope specific monocyte chemotactic protein-1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001386

A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
monocyte chemotactic protein-1 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
monocyte chemotactic protein-1 production c
epitope specific cytokine production by T cells c

epitope specific perforin production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001502

The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope.
has super-classes
perforin production c
perforin production c and (process is result of op some MHC:epitope complex binding to TCR c)

epitope specific RANTES production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001366

A process of RANTES production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
chemokine (C-C motif) ligand 5 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
chemokine (C-C motif) ligand 5 production c
epitope specific cytokine production by T cells c

epitope specific T cell activationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001208

A process of T cell activation resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
T cell activation c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
T cell activation c

epitope specific T cell enhancement of B cell mediated immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001314

A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
helper T cell enhancement of B cell mediated immune response c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
helper T cell enhancement of B cell mediated immune response c

epitope specific T cell proliferationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110182

A biological process where T cells proliferate resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
T cell proliferation c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
T cell proliferation c

epitope specific T cell tolerance inductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001249

A process of T cell tolerance induction resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
T cell tolerance induction c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
T cell tolerance induction c
epitope specific tolerance induction by T cells c

epitope specific TNF release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110206

A biological process where T cells produce TNF resulting from the recognition of a T cell epitope.
Source
IEDB
is equivalent to
tumor necrosis factor production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
tumor necrosis factor production c
epitope specific tumor necrosis factor superfamily cytokine production by T cells c

epitope specific tolerance induction by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001201

A process of tolerance induction by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
tolerance induction c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
tolerance induction c
has sub-classes
epitope specific T cell tolerance induction c

epitope specific transforming growth factor-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001267

A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
transforming growth factor beta production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
transforming growth factor beta production c
epitope specific cytokine production by T cells c

epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001518

A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
tumor necrosis factor (ligand) superfamily member 11 production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
tumor necrosis factor (ligand) superfamily member 11 production c
epitope specific tumor necrosis factor superfamily cytokine production by T cells c

epitope specific tumor necrosis factor superfamily cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001351

A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
tumor necrosis factor superfamily cytokine production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
tumor necrosis factor superfamily cytokine production c
epitope specific cytokine production by T cells c
has sub-classes
epitope specific TNF release by T cells c, epitope specific lymphotoxin A production by T cells c, epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells c

epitope specific type IV hypersensitivity by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001212

A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
type IV hypersensitivity c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
type IV hypersensitivity c

epitope specific vascular endothelial growth factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001612

A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope.
Source
IEDB (QTT)
is equivalent to
vascular endothelial growth factor production c and (process is result of op some MHC:epitope complex binding to TCR c)
has super-classes
vascular endothelial growth factor production c
epitope specific cytokine production by T cells c

epitope tolerance induction experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001488

An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response
Source
IEDB
has super-classes
efficacy of epitope intervention experiment c

epitope treatment experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001190

an epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host.
has super-classes
efficacy of epitope intervention experiment c

Epstein Barr virus transformed B cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100010

A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
Source
GROUP: OBI Biomaterial Branch
Example
PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
is equivalent to
(is_specified_output_of op some establishing cell culture c and (has_specified_input op some Viruses c)) and (derives from op only B cell c)
has super-classes
processed material c

equilibrium association constant (KA)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001548

A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
Source
IEDB
Example
KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
has super-classes
binding constant c

equilibrium dissociation constant (KD)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001536

A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
Source
IEDB
Example
KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb
has super-classes
binding constant c
has measurement unit label op some concentration unit c

equilibrium dissociation constant (KD) approximated by EC50c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001581

A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand.
Source
Assay Development: Fundamentals and Practices, By Ge Wu, page 74
has super-classes
binding constant c
half maximal effective concentration (EC50) c

equilibrium dissociation constant (KD) approximated by IC50c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001571

A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor.
Source
http://dx.doi.org/10.1016/0006-2952(73)90196-2
has super-classes
binding constant c
half maximal inhibitory concentration (IC50) c

error corrected data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000662

A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
is equivalent to
is_specified_output_of op some error correction data transformation c
has super-classes
data set c

error correction data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000668

An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
Source
EDITORS
is equivalent to
achieves_planned_objective op some error correction objective c
has super-classes
data transformation c
has sub-classes
multiple testing correction method c

error correction objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200186

An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
Source
PERSON: James Malone
Example
Application of a multiple testing correction method
has super-classes
correction objective c
has sub-classes
multiple testing correction objective c

erythrocytec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000232

A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
has super-classes
cell c

esophagus mucosac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002469

A mucosa that is part of a esophagus [Automatically generated definition].
has super-classes
material anatomical entity c

esophagus mucosa specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002532

A specimen that is derived from esophagus mucosa.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some esophagus mucosa c))
has super-classes
specimen from organism c

esophagus muscularis mucosac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0004648

A muscularis mucosa that is part of a esophagus.
has super-classes
tissue c

esophagus muscularis mucosa specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002535

A specimen that is derived from esophagus muscularis mucosa.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some esophagus muscularis mucosa c))
has super-classes
specimen from organism c

eSource documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000158

an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures
Source
article-without-pmid-or-doi:CDISCglossary
has super-classes
information content entity c

establishing cancer cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000867

is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal
Helen Parkinson
Source
Example
Establishment of HeLa immortal cell line
has super-classes
establishing cell line c
has_specified_output op some cancer cell line c

establishing cell culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600036

a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
Source
PERSON:Matthew Brush
has super-classes
material processing c
has_specified_input op some cell c
has_specified_input op some culture medium c
has_specified_output op some cultured cell population c
achieves_planned_objective op some material transformation objective c
has sub-classes
establishing cell line c, establishing primary cell culture c

establishing cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001867

a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
Source
PERSON:Matthew Brush
has super-classes
establishing cell culture c
has_specified_output op some cell line c
has sub-classes
cell line immortalization c, establishing cancer cell line c

establishing primary cell culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001878

an establishing cell culture process whereby cells explanted directly from an organismal source or specimen, and placed in culture for maintenance or propagation as a primary cell culture
Cells are originally plated at a certain concentration referred to as seeding density. Upon a first passage this primary culture becomes a secondary cell culture that can be propagated to become a stable and homogneous cell line. This class covers establishment of primary cultures from any native cell - 'in vivo' cells isolated from some multicellular organism, or 'in environment' unicellular organisms isolated from some natural environment.
Source
PERSON: Matthew Brush
Example
Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages. Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488 When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium.
has super-classes
establishing cell culture c
has_specified_output op some primary cultured cell population c

ethical standard compliance rulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500025

an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur
Source
PRS
has super-classes
standard compliance rule c

ethylenediaminetetraacetic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_42191

A polyamino carboxylic acid that has formula C10H16N2O8.
has super-classes
molecular entity c

Euarchontogliresc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_314146

has super-classes
Mammalia c
has sub-classes
Homo sapiens c, Rodentia c

euclidean distance calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200114

An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered.
Source
PERSON: Elisabetta Manduchi
has super-classes
similarity calculation c

Eukaryotac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2759

has super-classes
organism c
has sub-classes
Arabidopsis thaliana c, Dictyostelium discoideum c, Opisthokonta c

Euteleostomic back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_117571

has super-classes
Vertebrata <Metazoa> c
has sub-classes
Danio rerio c, Tetrapoda c

evaluant rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000067

a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Source
OBI
Example
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has super-classes
role c
inheres in op some material entity c
realized in op only assay c

evaporative light scattering detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000547

The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas.
Source
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082
has super-classes
measurement device c
has function op some measure function c

ex vivo designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001211

A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
Source
MO_808 ex_vivo_design
has super-classes
study design c

excisionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600022

the use physical means to remove a portion of a substance from the rest
Source
www.crohnsresource.com/glossary.jsp (via google define:resection)
Example
Cutting out the portion of a gel which contains a DNA fragment
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c

excitation functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000374

A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
has super-classes
function c
has sub-classes
light emission function c

exclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500028

an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
Source
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
Example
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
has super-classes
eligibility criterion c

exome sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002118

A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons).
Source
http://www.ncbi.nlm.nih.gov/pubmed/25827230
Example
DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified.
has super-classes
DNA sequencing c

expectation maximizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200053

EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function.
Source
PERSON: James Malone
has super-classes
probabilistic algorithm c

experimental disease inductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600030

a protocol application to induce a specific disease in an organism
Source
OBI branch derived
Example
the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome.
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

experimental infection of cell culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110030

is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture
Source
IEDB
has super-classes
adding substance to cell culture c
realizes op some material to be added role c and (inheres in op some infectious agent c)

experimentally modified cell in vitroc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000578

A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
has super-classes
cell c
processed material c
is_specified_output_of op some material processing c
has sub-classes
cultured cell c

exponential basec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200151

The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1).
Source
WEB: http://en.wikipedia.org/wiki/Exponential_function
has super-classes
mathematical feature c
has_feature_value dp some float

exponential transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200095

An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function.
Source
WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function
WEB: http://en.wikipedia.org/wiki/Exponential_function
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

exposure of material to environmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600009

a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input.
Source
IEDB
Example
Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber.
has super-classes
planned process c
has sub-classes
acclimatization c, waiting c

exposure resulting in immune reactivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110061

a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity
Source
IEDB
has super-classes
biological_process c

extracellular electrophysiology recordingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000454

An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data
Source
PERSON: Frank Gibson
Example
The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron
has super-classes
assay c
has_specified_output op some measurement datum c and (is about op some ion channel activity c)
achieves_planned_objective op some assay objective c
has sub-classes
measuring neural activity in the caudate nucleus c

extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000423

an extract is a material entity which results from an extraction process
Source
GROUP: OBI Biomatrial Branch
Example
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
has super-classes
processed material c
is_specified_output_of op some extraction c
has sub-classes
nucleic acid extract c, protein extract c

extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302884

A material separation in which a desired component of an input material is separated from the remainder
Example
nucleic acid extraction using phenol chloroform
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c
has sub-classes
nucleic acid extraction c

F mating typec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001347

A bacterial mating type indicating the presence of F plasmid in a bacterial cell.
has super-classes
biological sex c

F minus mating typec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001348

A bacterial mating type indicating the absence of F plasmid in a bacterial cell.
has super-classes
biological sex c

FACS Caliburc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400036

The FACS Calibur is one of the most popular cytometers in use for research.
Source
"http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11"
Example
"FACS Calibur at TFL, BCCRC, Vancouver"
has super-classes
flow cytometer sorter c

FACS Cantoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400037

A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications.
Source
http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf
has super-classes
flow cytometer analyzer c

FACS Canto2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400038

A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications.
Source
http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01
has super-classes
flow cytometer analyzer c

FACS Scanc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400039

A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications.
Source
http://www.brc.ubc.ca/brc/facs.html
has super-classes
flow cytometer analyzer c

FACSAriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400040

A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters.
Source
http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf
Example
FACSAria at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

FACSvantagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400041

The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells.
Source
http://www.bdbiosciences.com/features/products/display_product.php?keyID=42
Example
FACSvantage at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

factorial designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500014

factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
Source
http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
Example
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
has super-classes
study design c
has sub-classes
2x2 factorial design c, balanced incomplete block design c, fractional factorial design c

false discovery rate correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200163

The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
Source
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate
is equivalent to
has_specified_output op some q-value c
has super-classes
multiple testing correction method c
has_specified_input op some p-value c
achieves_planned_objective op some multiple testing correction objective c
has sub-classes
Benjamini and Hochberg false discovery rate correction method c, Benjamini and Yekutieli false discovery rate correction method c

family history designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001329

A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
Source
MO_544 family_history_design
has super-classes
study design c
has part op some organism feature identification objective c

family wise error rate correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200073

A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
Source
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
is equivalent to
has_specified_output op some FWER adjusted p-value c
has super-classes
multiple testing correction method c
achieves_planned_objective op some multiple testing correction objective c
has sub-classes
Holm-Bonferroni family-wise error rate correction method c, Westfall and Young family wise error rate correction c

far-Western blotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001669

is a adaptation on the western blot assay to explore protein-protein interaction. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody.
Source
adapted from ECO, PMID:18079728
Example
Studying protein-protein interactions via blot overlay or Far Western blot. Hall RA. Methods Mol Biol. 2004;261:167-74. Review. PMID: 15064457
is equivalent to
(assay c and (has_specified_input op some protein complex c) and (has_specified_output op some data item c and (is about op some protein domain specific binding c))) and (achieves_planned_objective op some assay objective c)
has super-classes
binding assay c

Faraday cagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001002

A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields.
Source
Wikipedia http://en.wikipedia.org/wiki/Faraday_cage
has super-classes
physical store c
has function op some environment control function c

FC 500c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400042

A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications.
Source
http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp
has super-classes
flow cytometer analyzer c

Fe-BABE RNA structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001023

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-BABE as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID: 7862644
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some (S)-1-(4-bromoacetamidobenzyl)EDTA c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

feature extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001028

A planed process with objective of obtaining quantified values from an image.
Source
MO_928: feature_extraction
has super-classes
data transformation c
has_specified_input op some image c
has_specified_output op some data item c
achieves_planned_objective op some feature extraction objective c

feature extraction objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200005

A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
Source
TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction
has super-classes
data transformation objective c

fecesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001988

Portion of semisolid bodily waste discharged through the anus[MW,modified]
has super-classes
organism substance c

feces specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002503

A specimen that is derived from feces.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some feces c))
has super-classes
specimen from organism c

feed rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000248

a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment.
Source
OBI
Example
Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008
has super-classes
complete nutrient role c

femalec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000383

A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
has super-classes
biological sex c

fertilizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0009566

The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
has super-classes
biological_process c

fiat objectc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000024

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
has super-classes
material entity c

fibroblastc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000057

A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
has super-classes
cell c

figurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000308

An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
Example
Any picture, diagram or table
has super-classes
information content entity c
has sub-classes
diagram c, image c

filled capsulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000821

A pill in the form of a small rounded gelatinous container with medicine inside.
Source
http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n
has super-classes
pill c
has part op some capsule shell c

filter functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000378

A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
has super-classes
material separation function c
has sub-classes
gas filter function c, liquid filter function c

filter paperc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000151

a device manufacture with the intent to provide a porous unsized paper used for filtering.
Source
sep:00107
has super-classes
material separation device c
has function op some filter function c

filtrationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302885

filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
Source
OBI-Branch: adapted from wikipedia and wordnet
Example
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c
has participant op some filter paper c

Fisher's exact testc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200176

Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests.
Source
WEB:http://mathworld.wolfram.com/FishersExactTest.html
has super-classes
statistical hypothesis test c
achieves_planned_objective op some statistical hypothesis test objective c

flame ionization detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000521

A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample.
Source
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197
has super-classes
gas chromatography detector c

flame photometric detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000588

The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected.
Source
WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091
has super-classes
gas chromatography detector c

flash freezingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001952

A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C.
Source
WEB: http://en.wikipedia.org/wiki/Flash_freezing
has super-classes
freezing c

flash pump systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000557

Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048
has super-classes
chromatography pump system c

flow cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400043

Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
Source
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
Example
Biofilm Flow Cell
has super-classes
container c
has function op some contain function c
has sub-classes
quartz cuvette flow chamber c

flow cytometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400044

A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
Source
http://en.wikipedia.org/wiki/Flow_cytometer
Example
FACS Calibur
has super-classes
cytometer c
(has part op some flow cell c) and (has part op some light source c) and (has part op some optical filter c) and (has part op some photodetector c)
has part op some obscuration bar c
has part op some droplet sorter c
has sub-classes
flow cytometer analyzer c, flow cytometer sorter c

flow cytometer analyzerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400008

An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis.
Source
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
Example
FACS Calibur, Luminex 100
has super-classes
flow cytometer c
has part op some flow cell c
has part op some light source c
has part op some optical filter c
has part op some photodetector c
has function op some measure function c
has sub-classes
A10-Analyzer c, A40-MiniFCM c, Bactiflow c, CYFlow ML c, Cell Lab Quanta SC c, CyFlow SL c, CyFlow SL3 c, Cyan c, CytoBuoy flow cytometer analyzer c, CytoSence c, CytoSub c, FACS Canto c, FACS Canto2 c, FACS Scan c, FC 500 c, Guava EasyCyte Mini c, Guava EasyCyte Plus c, Guava Personal Cell Analysis c, Guava Personal Cell Analysis-96 c, LSRFortessa X-20 c, Luminex 100 c, Luminex 200 c, MACS Quant c, SomaScope c, Somacount c, inFlux Analyzer c

flow cytometer sorterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400099

A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest.
Source
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
Example
BioSorter2000, LSR2
has super-classes
material separation device c
flow cytometer c
has part op some light source c
has part op some optical filter c
has part op some photodetector c
has part op some droplet sorter c
has function op some material separation function c
has sub-classes
BioSorter1000 c, BioSorter2000 c, BioSorter250 c, BioSorter500 c, CyFlow Space c, FACS Calibur c, FACSAria c, FACSvantage c, Influx Cell Sorter c, LSR2 c, MoFlo c, Reflection c

flow cytometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000916

A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution.
Source
IEDB
Example
Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
is equivalent to
cytometry assay c and ((realizes op some function c and (inheres in op some flow cytometer c)) and (has_specified_input op some flow cytometer c)) and (has part op some fluorescence detection assay c)
has super-classes
cytometry assay c

flow cytometry assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001659

A B cell epitope qualitative binding to antibody assay that uses a flow cytometry assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some flow cytometry assay c)
has super-classes
fluorescence detection binding assay c
assay measuring qualitiative binding of a B cell epitope:antibody complex c

flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001317

A T cell epitope qualitative binding assay that uses a cell-cell binding detection by flow cytometry assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex c and (has part op some flow cytometry assay c)
has super-classes
fluorescence detection binding assay c
assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex c
has sub-classes
MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex c

flow high resolution probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000527

Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195
has super-classes
Bruker high resolution probe c

flow probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000519

An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes.
Source
WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131
has super-classes
NMR probe c

fluid flow ratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0002243

A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time.
has super-classes
quality of a single physical entity c

fluid pressure regulatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400045

Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
LSR2 fluid pressure regulator
has super-classes
measurement device c
physical store c
has function op some environment control function c
has function op some measure function c

fluoresceinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_31624

A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy.
has super-classes
molecular label c
has role op some molecular label role c

fluorescencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000018

A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
has super-classes
disposition c

fluorescence compensation matrixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000213

A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix.
Source
group:Flow Cytometry community
Example
((1.053096, -0.22476), (-0.24877, 1.053096))
has super-classes
information content entity c

fluorescence detection assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001501

An assay in which a material's fluorescence is determined.
Source
IEDB
Example
Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
is equivalent to
assay c and ((realizes op some fluorescence c) and (has_specified_input op some material entity c)) and (has_specified_output op some is about op some fluorescence c)
has super-classes
assay c

fluorescence detection binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001499

binding assay that uses fluorescence detection as an indicator of binding
Source
IEDB
is equivalent to
binding assay c and (has part op some fluorescence detection assay c)
has super-classes
binding assay c
has sub-classes
cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection c, cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection c, cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection c, cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection c, cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection c, cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection c, cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection c, cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection c, cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection c, cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection c, cell-cell binding detection by flow cytometry assay c, flow cytometry assay measuring binding of a B cell epitope:antibody complex c, flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex c, fluorescence quenching binding assay c, purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection c, purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection c, purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection c, purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection c, quenching assay measuring binding of a B cell epitope:antibody complex c, quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex c, quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex c, quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex c

fluorescence quenching binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001979

A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other.
Source
IEDB
has super-classes
fluorescence detection binding assay c
has part op some fluorescence detection assay c
has sub-classes
antibody binding detection by fluorescence quenching c

fluorescene detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000563

A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected.
Source
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080
has super-classes
measurement device c
has function op some measure function c

fluorescent reporter intensityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000010

A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
Source
group:OBI
has super-classes
measurement datum c

fluorescently labeled MHC multimerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000788

A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand
has super-classes
molecular-labeled material c
has part op some molecular label c
is_specified_output_of op some addition of molecular label c
bearer of op some fluorescence c

fluorine-induced chemiluminescence detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000617

A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator.
Source
WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087
has super-classes
gas chromatography detector c

fluorometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400143

A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample.
Source
OBI
Example
laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300
has super-classes
spectrophotometer c
has sub-classes
portable fluorometer c

footnotec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000325

A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
Example
The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
has super-classes
document part c
is about op some document part c

formaldehyde-assisted isolation of regulatory elements assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001859

An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity.
Source
http://en.wikipedia.org/wiki/FAIRE-Seq
Example
Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877–85. [PMID:17179217]
has super-classes
DNA sequencing c
has part op some DNA sequencing c
has part op some library preparation c
has part op some cross linking c
has_specified_input op some deoxyribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some protein and DNA interaction identification objective c
has participant op some DNA sequencer c
has participant op some sonicator c

forward PCR primerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001946

A short oligonucleotide complementary to target DNA (5'->3' on plus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm.
Source
adapted from http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p
Example
SP6 promoter, forward primer (SP6 TTTAGGTGACACTATAG)
has super-classes
deoxyribonucleic acid c
reagent c
deoxyribonucleic acid c and (has role op some reagent role c)
(has part op some deoxyribonucleic acid c) and (is_specified_input_of op some polymerase chain reaction c or real time polymerase chain reaction assay c or real time reverse-transcription polymerase chain reaction assay c)

fourier transformation NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000487

In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation.
Source
GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284
has super-classes
NMR instrument c

fraction collectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000536

A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing.
Source
WEB:<http://www.chromatography-online.org/topics/fraction/collector.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073
has super-classes
chromatography instrument c

fractional factorial designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500016

A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
Source
http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
has super-classes
factorial design c

freeze functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000375

A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
has super-classes
function c

freeze substitution systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001127

A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins.
Source
doi:10.1017/S143192760707866X
has super-classes
device c
has function op some freeze function c
has function op some mechanical function c

freezingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001953

A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities.
Source
Mathias Brochhausen
has super-classes
planned process c
has sub-classes
flash freezing c

freezing storagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000915

A storage process in temperature that maintenance the frozen status of the stored entities.
Source
MO_481 frozen_storage
OBI
Example
a fozen pellet used for later assay
has super-classes
storage c
(has_specified_input op some material entity c and (has quality op some frozen c)) and (has_specified_output op some material entity c and (has quality op some frozen c))
achieves_planned_objective op some material maintenance objective c

frequency unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000105

A unit which is a standard measure of the number of repetitive actions in a particular time.
has super-classes
measurement unit label c
has members
hertz ni

fresh specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000971

a specimen that is output of a specimen creation process used for an investigation without storage.
Source
MO_730 fresh_sample
Example
a liver freshly removed from a rat
has super-classes
specimen with known storage state c
is disjoint with
frozen specimen c, paraffin specimen c, lyophilized specimen c, agar stab specimen c

frozenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001985

A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
has super-classes
quality of a single physical entity c

frozen specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000922

A specimen that has been frozen in order to store it.
Source
MO_610 frozen_sample
Example
Frozen blood plasma
is equivalent to
(is_specified_output_of op some freezing storage c and (has_specified_input op some has role op some specimen role c)) and (has role op some specimen role c)
has super-classes
specimen with known storage state c
is disjoint with
paraffin specimen c, lyophilized specimen c, fresh specimen c, agar stab specimen c

fucoidanc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000817

Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber).
Source
http://en.wikipedia.org/wiki/Fucoidan
has super-classes
molecular entity c

functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000034

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
has super-classes
disposition c
has sub-classes
adaptive immune effector function c, antigen presentation function c, connection function c, consume data function c, contain function c, cool function c, current amplification function c, energy supply function c, environment control function c, excitation function c, freeze function c, heat function c, information processor function c, injection function c, ionization function c, magnify function c, material combination function c, material separation function c, measure function c, mechanical function c, molecular_function c, perturb function c, reagent application function c, record function c, solid support function c, specimen fixation function c, stabilization function c, sterilization function c, synthesizing function c, transfer function c
is in domain of
function of op
is in range of
has function op

fuzzy clustering objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000653

A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori.
Source
PERSON: James Malone
PERSON: Ryan Brinkman
has super-classes
data transformation objective c

FWER adjusted p-valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001265

A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
Source
adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
Example
http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
has super-classes
quantitative confidence value c

gadodiamidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_37333

A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
has super-classes
molecular entity c

gadodiamide hydratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_31642

The hydrate of gadodiamide.
has super-classes
molecular entity c

gadolinium atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33375

A lanthanoid atom that has formula Gd.
has super-classes
molecular entity c

gadolinium molecular entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_35729

has super-classes
molecular entity c

gadoteridolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_31643

A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
has super-classes
molecular entity c

Gallus gallusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_9031

has super-classes
Amniota c

gamma counterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000059

A processed material which measures gamma radiation
Source
http://en.wikipedia.org/wiki/Gamma_counter
Example
A Geiger counter
has super-classes
measurement device c
has function op some measure function c

gas chromatography detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000637

A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors.
Source
WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083
has super-classes
chromatography detector c
has sub-classes
atomic emission detector c, electron capture detector c, flame ionization detector c, flame photometric detector c, fluorine-induced chemiluminescence detector c, mass selective detector c, nitrogen phosphorous detector c, ozone-induced chemiluminescence detector c, photoionization detector c, thermal conductivity detector c

gas chromatography equipmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000542

Any device used in a gas chromatography experiment.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030
has super-classes
chromatography device c
has sub-classes
gas chromatography oven c, gas generator c, gas purifier c

gas chromatography mass spectrometryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200199

Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds.
Source
PERSON: Tina Boussard
has super-classes
mass spectrometry analysis c
achieves_planned_objective op some spectrum analysis objective c

gas chromatography ovenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000554

A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039
has super-classes
gas chromatography equipment c

gas filter functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000380

A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture
has super-classes
filter function c

gas generatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000507

An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century.
Source
WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033
has super-classes
gas chromatography equipment c
has sub-classes
hydrogen generator c, nitrogen generator c

gas laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400047

A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas.
Source
John Quinn
http://en.wikipedia.org/wiki/Gas_laser
Example
helium-neon gas laser used to erradiate cells in a flow cytometer.
has super-classes
laser c
has sub-classes
ion laser c, metal vapor laser c

gas purifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000638

Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems.
Source
WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036
has super-classes
gas chromatography equipment c

gatingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200077

Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry.
Source
PERSON: James Malone
PERSON: Josef Spidlen
PERSON: Richard Scheuermann
PERSON: Ryan Brinkman
PERSON:Melanie Courtot
has super-classes
partitioning data transformation c
data vector reduction data transformation c
achieves_planned_objective op some data vector reduction objective c
achieves_planned_objective op some partitioning objective c

gel dryerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000404

A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels
Source
sep:00094
has super-classes
physical store c
has function op some contain function c
has function op some environment control function c

gel electrophoresis systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001121

A device that moves charged particles through a medium by using an electric field induced by electrodes.
Source
http://en.wikipedia.org/wiki/Category:Electrophoresis
has super-classes
electrophoresis system c
has sub-classes
pulsed-field gel electrophoresis system c

gel filtration columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000535

A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104
has super-classes
size exclusion column c

gel imaging systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001081

A device that is used to acquire images of laboratory gels.
Source
PERSON: Erik Segerdell
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

gel permeation columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000622

A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size.
Source
WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103
has super-classes
chromatography column c

gel tankc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400140

a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
Source
sep:00095
Example
CHEF gel box, slab gel box, capillary electrophoresis
has super-classes
physical store c
has function op some contain function c
has function op some environment control function c

GenBank IDc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001614

A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
Source
NIAID GSCID-BRC metadata working group
has super-classes
centrally registered identifier symbol c
denotes op only sequence data c

gene dosage assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001022

an assay of changes in phenotype due to increased or decreased dosage of a single allele of a gene.
Source
David Osumi Sutherland
has super-classes
assay c

gene expressionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0010467

The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
has super-classes
biological_process c

gene knock inc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001149

a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
Source
MO_437 gene_knock_in
WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
has super-classes
genetic transformation c

gene knock outc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001148

a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
Source
MO_771 gene_knock_out
has super-classes
genetic transformation c

gene knock-down assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001672

is an assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells.
Source
PMID:17430206
is equivalent to
(assay c and (has_specified_input op some cultured cell population c) and (has_specified_output op some data item c and (is about op some molecular_function c))) and (achieves_planned_objective op some assay objective c)
has super-classes
assay c

gene listc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000118

A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
Source
group:OBI
Example
Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
has super-classes
data set c

gene list visualizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200191

Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type.
has super-classes
data visualization c
has_specified_output op some table c
has_specified_input op only gene list c

GenePattern softwarec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000713

a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
Source
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
has super-classes
software c
has members
GenePattern module CARTXValidation ni, GenePattern module HeatMapViewer ni, GenePattern module HierarchicalClustering ni, GenePattern module HierarchicalClusteringViewer ni, GenePattern module KMeansClustering ni, GenePattern module KNN ni, GenePattern module KNNXValidation ni, GenePattern module PCA ni, GenePattern module PeakMatch ni, GenePattern module SVM ni

generalized family wise error rate correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200160

A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer.
Source
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
has super-classes
multiple testing correction method c
achieves_planned_objective op some multiple testing correction objective c

generically dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000031

A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
has super-classes
continuant c
has sub-classes
information content entity c, region c
is in domain of
is concretized as op
is in range of
concretizes op
is disjoint with
independent continuant c, specifically dependent continuant c

genetic alteration informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001364

a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
Source
Group: OBI group
has super-classes
genetic characteristics information c
has sub-classes
allele information c

genetic characteristics informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001404

a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
Source
MO_66 IndividualGeneticCharacteristics
has super-classes
data item c
is about op some region c and (is concretized as op some inheres in op some nucleic acid c and (part of op some organism c))
has sub-classes
genetic alteration information c, genetic population background information c, genotype information c

genetic materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001868

A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants.
Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material. Qualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. Non-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells).
Source
OBI developer calls, March 4 2013 and March 11 2013
has super-classes
nucleic acid c
part of op some cell c or Viruses c

genetic modification designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001460

A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
Source
MO_447 genetic_modification_design
has super-classes
intervention design c
has part op some biological feature identification objective c
has part op some study design independent variable c and (is about op some study intervention c and genetic transformation c)

genetic population background informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001225

a genetic characteristics information which is a part of genotype information that identifies the population of organisms
Source
Group: OBI group
Example
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
has super-classes
genetic characteristics information c
part of op some genotype information c

genetic transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600043

the introduction. alteration or integration of genetic material into a cell or organism
Source
OBI branch derived
Example
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
has super-classes
material processing c
has_specified_output op some genetically modified material c
achieves_planned_objective op some genetic transformation objective c
has sub-classes
DNA transduction c, chromosomal substitution c, gene knock in c, gene knock out c, immortalizing cell line transformation c, induced mutation c, transfection c

genetic transformation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001153

a material transformation objective aims to create genetically modified organism or cell
Source
Person: Jie Zheng
has super-classes
material transformation objective c

genetically modified materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001151

a material entity, organism or cell, that is the output of a genetic transformation process.
Source
GROUP: OBI
is equivalent to
genetically modified organism c or (cell c and (is_specified_output_of op some genetic transformation c))
has super-classes
processed material c
has sub-classes
genetically modified organism c

genetically modified organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302859

an organism that is the output of a genetic transformation process
Source
OBI Biomaterial
Example
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
is equivalent to
organism c and (is_specified_output_of op some genetic transformation c)
has super-classes
genetically modified material c
organism c
has sub-classes
transgenic organism c

Genome Analyzer IIec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002027

An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories.
Source
http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf
has super-classes
Illumina Genome Analyzer II c

Genome Analyzer IIxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002000

An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.
Source
ENCODE group
Example
Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897
has super-classes
Illumina Genome Analyzer II c

genome coveragec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001939

A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%.
Source
A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. PMID: 22510764
Example
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "The genome coverage increased from 81.16% to 93.91%"
has super-classes
data item c
is about op some assembly c
is_specified_output_of op some sequence assembly process c

genotype informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001305

a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
Source
Group: OBI group
Example
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
has super-classes
genetic characteristics information c
(has part op some genetic population background information c) and (has part op some genetic alteration information c)
has sub-classes
wild type organism genotype information c

genotyping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000435

an assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
Source
OBI Biomaterial
Example
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
is equivalent to
has_specified_output op some genotype information c
has super-classes
analyte assay c
realizes op some analyte role c and (role of op some deoxyribonucleic acid c)
has_specified_input op some specimen c and (has part op some deoxyribonucleic acid c)
has_specified_output op some genotype information c
achieves_planned_objective op some sequence feature identification objective c
has sub-classes
PCR-SSCP assay c, comparative genomic hybridization by array assay c, genotyping by array assay c, genotyping by high throughput sequencing assay c, killer cell immunoglobulin-like receptor typing assay c, major histocompatibility typing assay c

genotyping by array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001274

An assay in which an array is used to detect polymorphisms in DNA samples
Source
EFO_0002767: genotyping by array
has super-classes
genotyping assay c
has participant op some DNA microarray c
has sub-classes
genotyping by SNP array c, genotyping by tiling array c

genotyping by array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001387

A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology.
Source
MO_560 genotyping_design
has super-classes
genotyping design c
is concretized as op some realized in op some (has part op some genotyping by array assay c) and (has participant op some DNA microarray c)

genotyping by high throughput sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001247

An assay in which high througput sequencer is used to detect polymorphisms in DNA samples
Source
EFO_0002771: genotyping by high throughput sequencing
has super-classes
genotyping assay c
has participant op some DNA sequencer c

genotyping by high throughput sequencing designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001200

A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
Source
MO_560 genotyping_design
has super-classes
genotyping design c
is concretized as op some realized in op some (has part op some genotyping by high throughput sequencing assay c) and (has participant op some DNA sequencer c)

genotyping by SNP arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002031

A genotyping by array assay that aims to detect variation in (mostly) genomic DNA of an organism, strain, etc relative to some reference sequence employing snp array technology.
Source
PMID:20393561
Example
PMID:20080586
has super-classes
genotyping by array assay c
has participant op some SNP microarray c

genotyping by tiling arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002030

A genotyping by array assay that aims to detect variation in (mostly) genomic DNA of an organism, strain, etc relative to some reference sequence employing tiling array technology.
Source
PMID:19521816
Example
PMID:19521816
has super-classes
genotyping by array assay c
has participant op some tiling microarray c

genotyping designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001444

A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
Source
MO_560 genotyping_design
has super-classes
study design c
has part op some sequence feature identification objective c
is concretized as op some realized in op some has part op some genotyping assay c
has sub-classes
genotyping by array design c, genotyping by high throughput sequencing design c

geographic locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GAZ_00000448

A reference to a place on the Earth, by its name or by its geographical location.
has super-classes
site c

geometric mean calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200001

A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations).
Source
PERSON: Mathias Brochhausen
has super-classes
center calculation data transformation c
descriptive statistical calculation data transformation c
(has_specified_output op some center value c) and (achieves_planned_objective op some center calculation objective c)
achieves_planned_objective op some descriptive statistical calculation objective c

glass columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000609

A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101
has super-classes
chromatography column c

glial cell line-derived neurotrophic factorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000007928

A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof.
has super-classes
protein c

global modularity calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200054

A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network.
Source
PERSON: Richard Scheuermann
has super-classes
network graph quality calculation c

glucometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000795

A measurement device with the function to measure and record the level/amount of glucose in a blood sample
Source
http://en.wikipedia.org/wiki/Glucose_meter
Example
Diabetic patients use glucometers to determine their glucose levels
has super-classes
measurement device c
has function op some measure function c

glucosec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_17234

An aldohexose used as a source of energy and metabolic intermediate.
has super-classes
molecular entity c

glucose in solutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100086

A scattered aggregate of glucose molecules in a liquid
Example
Glucose present in blood
has super-classes
material entity c
has grain op only glucose c

glucose metabolic processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0006006

The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
has super-classes
biological_process c

glucose tolerance testc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000721

is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
Source
NuGO OBI plan branch
Example
PMID: 19527607 Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus. Lin CH, Wen SF, Wu YH, Huang MJ. Chang Gung Med J. 2009 May-Jun;32(3):283-9.
has super-classes
assay c
has part op some measuring glucose concentration in blood serum c and (realizes op some concretizes op some study design dependent variable c)
has part op some data transformation c and (has_specified_input op some measurement datum c) and (has_specified_output op some graph c)
has part op some administering substance in vivo c and (has_specified_input op some glucose c)
realizes op some concretizes op some study design independent variable c
has_specified_output op some information content entity c and (is_proxy_for op some Insulin resistance c)
achieves_planned_objective op some biological feature identification objective c
achieves_planned_objective op some assay objective c

gradient pump systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000573

A pump system optimized for gradient chromatography.
Source
WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050
has super-classes
chromatography pump system c

gradient separationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600051

a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities
Source
OBI branch derived
Example
the use of a sucrose gradient to isolate mitochondria
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c

graeco latin square designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500012

Greco-Latin square design is a study design which relates to Latin square design
Source
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
Example
PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
has super-classes
randomized complete block design c

grantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001636

A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role.
Source
OBI
has super-classes
plan specification c
part of op some study design c

grant agencyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001942

An organization that provides funding support for projects such as investigations.
Source
NIAID GSCID-BRC metadata working group
has super-classes
organization c

grant identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001629

A CRID symbol used to identify a grant.
Source
NIAID GSCID-BRC metadata working group
has super-classes
centrally registered identifier symbol c
denotes op only grant c

granulocyte colony-stimulating factor productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071611

The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific granulocyte colony stimulating factor production by T cells c

granulocyte macrophage colony-stimulating factor productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032604

The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific GM-CSF release by T cells c

granulysin productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0036262

The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
biological_process c
has sub-classes
epitope specific granulysin production by T cells c

granzyme A productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0035746

The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
biological_process c
has sub-classes
epitope specific granzyme A production by T cells c

granzyme B productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071613

The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
biological_process c
has sub-classes
epitope specific granzyme B production by T cells c

graphc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000038

A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
Source
OBI_0000240
group:OBI
has super-classes
diagram c
has sub-classes
Venn diagram c, contour plot c, dendrogram c, density plot c, dot plot c, graph of vertices c, heatmap c, histogram c, line graph c, scatter plot c

graph of verticesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000714

A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix.
Source
WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
Example
For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
has super-classes
graph c

group assignmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600015

group assignment is a process which has an organism as specified input and during which a role is assigned
Source
OBI Plan
Example
Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
has super-classes
planned process c
has_specified_input op some organism c
has_specified_output op some role c and (inheres in op some organism c)
has sub-classes
group randomization c

group randomizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302900

A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
Source
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
Example
PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
has super-classes
group assignment c

growth condition intervention designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000985

A study design in which the independent variable is the environmental condition in which the specimen is growing
Source
MO_588 growth_condition_design
has super-classes
intervention design c
has part op some study design independent variable c and (is about op some study intervention c)
has part op some study design independent variable c and (is about op some growth environment c)

growth environmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000997

The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
Source
OBI group
has super-classes
material entity c
has sub-classes
atmosphere c

guanyl-specific ribonuclease T1c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000025467

A protein that is a translation product of the Aspergillus oryzae rntA gene or a 1:1 ortholog thereof.
has super-classes
protein c

guar gumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000814

Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder.
Source
http://en.wikipedia.org/wiki/Guar_gum
has super-classes
material entity c

guard columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000614

Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111
has super-classes
chromatography device c

Guava EasyCyte Minic back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400048

A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement.
Source
http://www.guavatechnologies.com/main/products/easyCyteMini.cfm
has super-classes
flow cytometer analyzer c

Guava EasyCyte Plusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400049

A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement.
Source
http://www.guavatechnologies.com/main/products/easycyte-new.cfm
has super-classes
flow cytometer analyzer c

Guava Personal Cell Analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400050

A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement.
Source
http://www.guavatechnologies.com/main/products/PCA-new.cfm
has super-classes
flow cytometer analyzer c

Guava Personal Cell Analysis-96c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400051

The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement.
Source
http://www.guavatechnologies.com/main/products/PCA-96new.cfm
has super-classes
flow cytometer analyzer c

h minusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001345

A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus.
has super-classes
biological sex c

h plusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001346

A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus.
has super-classes
biological sex c

hair specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002517

A specimen that is derived from hair.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some strand of hair c))
has super-classes
specimen from organism c

half life datum (t 1/2)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001171

The time it takes for 50% of a class of stochastic processes to occur.
Source
Bjoern Peters
has super-classes
time measurement datum c
has measurement unit label op some time unit c
has sub-classes
half life of binding datum c

half life of binding datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001583

A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association.
Source
IEDB
Example
The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate.
has super-classes
binding constant c
half life datum (t 1/2) c

half maximal effective concentration (EC50)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001180

half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time.
Source
wikipedia
Example
Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed.
has super-classes
scalar measurement datum c
has measurement unit label op some concentration unit c
is about op some dose response curve c
has sub-classes
equilibrium dissociation constant (KD) approximated by EC50 c

half maximal inhibitory concentration (IC50)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001191

Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect.
Source
wikipedia
Example
Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
has super-classes
scalar measurement datum c
has measurement unit label op some concentration unit c
is about op some dose response curve c
has sub-classes
equilibrium dissociation constant (KD) approximated by IC50 c

handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0002201

A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
has super-classes
behavioral quality c
has sub-classes
ambidextrous handedness c, left handedness c, right handedness c

handedness assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000944

A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
Source
http://en.wikipedia.org/wiki/Handedness
Example
The Edinburgh handedness assay is a specific method of determing handedness
is equivalent to
assay c and (has_specified_output op some measurement datum c and (is about op some handedness c))
has super-classes
assay c
has sub-classes
Edinburgh handedness assay c, self reported handedness assessment c

handedness categorical measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000976

A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally
has super-classes
categorical measurement datum c
is quality measurement of op some handedness c
has category label op some { right handed , ambidexterous , left handed }

haploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001375

A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes.
has super-classes
ploidy c

hardware optimization objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000232

Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
has super-classes
hardware testing objective c

hardware testing designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001957

A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision.
Source
MO_734 hardware_variation_design
is equivalent to
study design c and (has part op some hardware testing objective c)
has super-classes
study design c
has part op some study design independent variable c and (is about op some device c)

hardware testing objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000134

Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
has super-classes
methodology testing objective c
has sub-classes
hardware optimization objective c

health care provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000207

a worker role of providing medical care either within or outside the study timeline
has super-classes
worker role c

heartc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000948

A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
has super-classes
material anatomical entity c

heart specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002520

A specimen that is derived from heart.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some heart c))
has super-classes
specimen from organism c

heat functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000371

A heat function is a function that increases the internal kinetic energy of a material
has super-classes
function c

heating blockc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400108

A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay
Source
MO
Example
An instrument used to heat and/or maintain material at a set temperature.
has super-classes
environmental control device c
has function op some heat function c

heatmapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000180

A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
Source
GROUP:OBI
has super-classes
graph c

HeLa cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110032

A cell line derived from human cervical cancer cells.
Source
IEDB
http://www.biotech.ist.unige.it/cldb/cl1597.html
has super-classes
immortal cell line c

Helicos sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000697

is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length.
Source
adapted from wikipedia
Example
PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9.
has super-classes
DNA sequencing by synthesis c
has participant op some HeliScope Single Molecule Sequencer c
immediately preceded by op some immobilization c

HeliScope Single Molecule Sequencerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000717

is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
has super-classes
DNA sequencer c
is_manufactured_by op value Helicos

helium cadmium ion laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400052

A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer.
Source
http://en.wikipedia.org/wiki/Laser#Gas_lasers
Example
KIMMON HeCd 325nm laser
has super-classes
metal vapor laser c

helium neon ion laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400053

A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm.
Source
John Quinn
http://en.wikipedia.org/wiki/Laser#Gas_lasers
Example
A helium neon laser can by used to irradiate cells in a flow cytometer.
has super-classes
ion laser c

helper T cell enhancement of adaptive immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0035397

Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
has super-classes
adaptive immune response c
has sub-classes
helper T cell enhancement of B cell mediated immune response c, helper T cell enhancement of T cell mediated immune response c

helper T cell enhancement of B cell mediated immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0035399

Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell.
has super-classes
helper T cell enhancement of adaptive immune response c
has sub-classes
epitope specific T cell enhancement of B cell mediated immune response c

helper T cell enhancement of T cell mediated immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0035398

Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell.
has super-classes
helper T cell enhancement of adaptive immune response c
has sub-classes
epitope specific helper T cell enhancement of T cell mediated immune response c

hematologyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000630

hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments
Source
OBI branch derived
Example
Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943
has super-classes
assay c
has_specified_output op some information content entity c and (is about op some hemopoiesis c)
achieves_planned_objective op some assay objective c

hemopoiesisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0030097

The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
has super-classes
biological_process c

hepatocytec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000182

The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
has super-classes
epithelial cell c

hepatocyte growth factor productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032605

The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

hermaphroditec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001340

A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
has super-classes
biological sex c

hierarchical clusteringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200042

A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
Source
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
has super-classes
class discovery data transformation c
(has_specified_output op some clustered data set c) and (achieves_planned_objective op some class discovery objective c)
has sub-classes
agglomerative hierarchical clustering c, divisive hierarchical clustering c
has members
GenePattern hierarchical clustering ni

high molecular weight DNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000834

The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
Source
OBI
Example
Extraction of chromosomal DNA from mammalian cells by first isolating nucei
has super-classes
DNA extract c

high performance liquid chromatography instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001057

A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
Source
http://en.wikipedia.org/wiki/High_performance_liquid_chromatography
has super-classes
liquid chromatography instrument c

high performance liquid chromotography assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002116

An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution.
Source
http://www.ncbi.nlm.nih.gov/pubmed/9491555
Example
On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml.
is equivalent to
analytical chromatography c and ((realizes op some function c and (inheres in op some high performance liquid chromatography instrument c)) and (has_specified_input op some high performance liquid chromatography instrument c))
has super-classes
analytical chromatography c

high resolution magic angle spin probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000607

Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192
has super-classes
Bruker high resolution probe c

high resolution probe with automatic tuning and matchingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000616

The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224
has super-classes
Bruker high resolution probe c

high temperature columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000574

A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233
has super-classes
chromatography column c

histamine secretion mediated by immunoglobulinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097280

Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface.
has super-classes
immune response c
has sub-classes
B cell epitope specific histamine secretion mediated by immunoglobulin c

histogramc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000179

A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
Source
GROUP:OBI
has super-classes
graph c

histological sample preparationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000341

histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
Source
OBI branch derived
has super-classes
material processing c
specimen collection process c
has_specified_input op some organ section c
achieves_planned_objective op some material transformation objective c
achieves_planned_objective op some specimen collection objective c
has participant op some microtome c

histologyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600020

the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement
Source
OBI branch derived
Example
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
has super-classes
assay c
has part op some imaging assay c
has part op some histological sample preparation c
has part op some staining c
has part op some collecting specimen from organism c
has_specified_output op some information content entity c and (is about op some cell c or organ section c)
achieves_planned_objective op some assay objective c

histone modificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0016570

The covalent alteration of one or more amino acid residues within a histone protein.
has super-classes
biological_process c

histone modification identification by ChIP-chip assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002016

A ChIP-chip assay to identify regions containing specific histones and their modifications.
Source
Penn group
has super-classes
ChIP-chip assay c
epigenetic modification assay c
has_specified_output op some information content entity c and (is about op some histone modification c)
achieves_planned_objective op some epigenetic modification identification objective c

histone modification identification by ChIP-Seq assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002017

A ChIP-seq assay to identify regions containing specific histones and their modifications.
Source
Penn group
has super-classes
ChIP-seq assay c
has_specified_output op some information content entity c and (is about op some histone modification c)
achieves_planned_objective op some epigenetic modification identification objective c

historyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000182

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
process c
is disjoint with
process profile c

Holm-Bonferroni family-wise error rate correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200066

a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction
Source
WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method
Example
t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179
has super-classes
family wise error rate correction method c
has_specified_input op some p-value c
has_specified_output op some FWER adjusted p-value c
achieves_planned_objective op some multiple testing correction objective c

Homo sapiensc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_9606

has super-classes
Euarchontoglires c
has sub-classes
Bioinformatics Resource Center contact person c, sequencing facility contact person c, specimen collector c, specimen provider principal investigator c

homogeneous polynomial transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200020

A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree.
Source
WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html
Example
a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables.
has super-classes
polynomial transformation c

homogenizerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400109

A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Source
http://en.wikipedia.org/wiki/Homogenizer
Example
mortar, blender
has super-classes
perturbation device c
has function op some perturb function c

hospitalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000844

A medical organization at which sick or injured people are given clinical care
Source
http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n
modified from the wording of the wordnet definition
Example
human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
has super-classes
organization c

host exposure to infectious agentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110003

a process in which an infectious agent comes into physical contact with a host organism.
Source
IEDB
is equivalent to
(has participant op some infectious agent c and (adjacent to op some host of immune response c)) and (has participant op some host of immune response c and (adjacent to op some infectious agent c))
has super-classes
biological_process c

host of immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110026

An organism in which an immune response process occurs.
Source
IEDB
Example
A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses.
is equivalent to
organism c and (has role op some host of immune response role c)
has super-classes
organism c

host of immune response rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110083

is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host.
Source
IEDB
has super-classes
role c
realized in op only immune response c or Immunization in vivo c

host rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000725

host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
Source
30 Mar09 submitted by vaccine community
OBI
http://en.wikipedia.org/wiki/Host_(biology)
Example
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
has super-classes
role c
inheres in op some organism c

Human 2.1M Whole-Genome CGH Tiling Array v2.0c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002011

A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features.
Source
http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
Example
Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274
has super-classes
tiling microarray c
is_manufactured_by op value Nimblegen

Human 3x720K Whole Genome CGH Tiling Arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002010

A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features.
Source
http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
Example
Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464
has super-classes
tiling microarray c
is_manufactured_by op value Nimblegen

Human 6x630K CGH Whole Genome Tiling Arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002109

A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features.
Source
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318
has super-classes
tiling microarray c
is_manufactured_by op value Nimblegen

human antithrombin-III (AT-III) in blood assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000787

An assay to measure the amount of antithrombin III in blood.
Source
WEB:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06
Example
PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit.
has super-classes
analyte assay c
(has_specified_input op some blood serum specimen c) and (has_specified_output op some scalar measurement datum c and (is about op some blood coagulation c)) and (achieves_planned_objective op some analyte measurement objective c)
realizes op some analyte role c and (role of op some scattered molecular aggregate c and (has grain op some antithrombin-III c))
has sub-classes
antithrombin-III (AT-III) berichrome assay c

Human Exon 1.0 ST tilling arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002025

A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay
Source
http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1
has super-classes
tiling microarray c
is_manufactured_by op value Affymetrix

Human Genome U133 Plus 2.0 tiling arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002023

A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants.
Source
http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292
has super-classes
tiling microarray c
is_manufactured_by op value Affymetrix

Human Genome U133 tiling arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002026

A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants.
Source
http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292
has super-classes
tiling microarray c
is_manufactured_by op value Affymetrix

human pathogenicity dispositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IDO_0000666

A disposition to initiate processes that result in a disorder in a human organism.
has super-classes
disposition c

human specimen setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002080

A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
Source
Duke Biobank, OBIB, OBI
is equivalent to
specimens collected in one encounter c and (derives from op some Homo sapiens c)
has super-classes
specimens collected in one encounter c

human subject enrollmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600004

A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
Source
IEDB
Example
enlisting familiy members of HIV patients into a study
has super-classes
selection c
has part op some informed consent process c
realizes op some concretizes op some eligibility criterion c
has_specified_input op some population c and (has part op some Homo sapiens c)
has_specified_output op some (population c and (has part op some Homo sapiens c)) and (has role op some participant under investigation role c)

hybridization chamberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400110

A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
Source
MO_563 hybridization_chamber
Example
Glass Array Hybridization Cassette
has super-classes
physical store c
has function op some contain function c
has function op some environment control function c

hybridization ovenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001075

A device that creates an appropriate environment for nucleic acid hybridization.
Source
PERSON: Erik Segerdell
has super-classes
incubator c
has function op some contain function c
has function op some mechanical function c

hybridization stationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400111

A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature.
Source
MO_497 hybridization station
Example
Labnet Problot12
is equivalent to
device c and (has part op some hybridization chamber c) and (has function op some environment control function c)
has super-classes
physical store c

hydrogen generatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000608

A gas generator that generates hydrogen gas.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035
has super-classes
gas generator c

hydrogen/deuterium exchange assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001976

An assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure.
Source
IEDB
Example
Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface.
has super-classes
assay c
(realizes op some reagent role c and (inheres in op some deuterium atom c)) and (has_specified_input op some deuterium atom c)

hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001997

A B cell epitope qualitative binding to antibody assay that uses a hydrogen/deuterium exchange assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some hydrogen/deuterium exchange assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

hydrogensulfitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_17137

A sulfur oxoanion that has formula HO3S.
has super-classes
molecular entity c

hydroxylc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_29191

An oxygen radical that has formula HO.
has super-classes
molecular entity c

hyper graeco latin square designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500013

PRS to do
Source
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
has super-classes
randomized complete block design c

hyperlog transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200008

A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation.
Source
ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42."
http://flowcyt.sourceforge.net/gating/latest.pdf
Example
This type of transformation is typically used in flow cytometry
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

hypersensitivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0002524

An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.
has super-classes
biological_process c
has sub-classes
B cell epitope specific hypersensitivity c, type IV hypersensitivity c

hypodermisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002072

Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
has super-classes
material anatomical entity c

hypothesis driven investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000355

is an investigation with the goal to test one or more hypothesis
Source
OBI branch derived
has super-classes
investigation c

hypothesis generating investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000356

is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
Source
OBI branch derived
has super-classes
investigation c

hypothesis textual entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000415

A textual entity that expresses an assertion that is intended to be tested.
Example
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has super-classes
textual entity c

Illumina BeadChipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001869

An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides.
Source
http://www.illumina.com/technology/beadarray_technology.ilmn
has super-classes
assay array c
is_manufactured_by op value Illumina
has sub-classes
1M-Duo Infinium HD BeadChip c, Illumina methylation BeadChip c

Illumina Genome Analyzer IIc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000703

is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
Source
Illumina Corporation
Example
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
has super-classes
DNA sequencer c
is_manufactured_by op value Illumina
has sub-classes
Genome Analyzer IIe c, Genome Analyzer IIx c

Illumina HiSeq 1000c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002022

A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
Source
http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
has super-classes
DNA sequencer c
is_manufactured_by op value Illumina

Illumina HiSeq 2000c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002001

A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.
Source
http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
Example
Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380
has super-classes
DNA sequencer c
is_manufactured_by op value Illumina

Illumina HiSeq 2500c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002002

A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.
Source
http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf
Example
Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882
has super-classes
DNA sequencer c
is_manufactured_by op value Illumina

Illumina HiSeq 3000c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002048

A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
Source
http://www.illumina.com/systems/hiseq-3000-4000.html
has super-classes
DNA sequencer c
is_manufactured_by op value Illumina

Illumina HiSeq 4000c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002049

A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
Source
http://www.illumina.com/systems/hiseq-3000-4000.html
has super-classes
DNA sequencer c
is_manufactured_by op value Illumina

Illumina methylation BeadChipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001870

A BeadChip made for an analyte assay that generates information about DNA methylation.
Source
Penn Group
is equivalent to
Illumina BeadChip c and (bearer of op some function c and (realized in op only assay c and (has_specified_output op some measurement datum c and (is about op some DNA methylation c))))
has super-classes
Illumina BeadChip c
has sub-classes
Methylation 27K BeadChip c, Methylation 450K BeadChip c

imagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000101

An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
Source
OBI_0000030
group:OBI
has super-classes
figure c
has sub-classes
photograph c

image acquisition functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000397

An image acquisition function is a function to acquire an image of a material
has super-classes
measure function c
inheres in op some image creation device c
realized in op only image creation c

image creationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001007

A planned process that captures an image of an object.
Example
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
has super-classes
planned process c
has_specified_input op some material entity c
has_specified_output op some image c
has sub-classes
array image creation c

image creation devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000398

An image creation device is a device which captures a digitized image of an object
Source
sep:00096
is equivalent to
device c and (has function op some image acquisition function c)
has super-classes
measurement device c
has sub-classes
SPECT scanner c, array scanner c, bead array reader c, computed tomography scanner c, digital camera c, gel imaging system c, image cytometer c, immunoblot scanner c, infrared image acquisition device c, microscope c, multispectral imaging flow cytometer c, positron emission tomography scanner c, radiography instrument c, small-animal image acquisition device c, ultrasound machine c

image cytometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400135

An image_cytometer is an instrument for image-based study or measurement of cells.
Source
http://web.mit.edu/solab/Research/ImageCytometry.html
Example
The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining.
has super-classes
image creation device c
has part op some light source c
has part op some optical filter c
has part op some photodetector c
has function op some image acquisition function c

imaging assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000185

An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
Source
OBI branch derived
has super-classes
assay c
has_specified_output op some image c
achieves_planned_objective op some assay objective c
has sub-classes
microscopy assay c

imaging NMR probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000539

An NMR probe that is designed for generating pictures from sample states via NMR imaging.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244
has super-classes
NMR probe c

immaterial entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000141

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
independent continuant c
has sub-classes
continuant fiat boundary c, site c, spatial region c
is in range of
has 2D boundary op
is disjoint with
material entity c

immobilizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302902

immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum.
Source
OBI-Branch
Example
PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23.
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

immortal cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0009828

A cell line that is expected to be capable of indefinite propagation in an vitro culture.
has super-classes
cell line c
has grain op some immortal cell line cell c
has grain op only immortal cell line cell c
has sub-classes
293-T cell line c, C1R cell line c, EL-4 cell line c, HeLa cell line c, JAWS II cell line c, JY cell line c, Jurkat cell line c, L cell line c, P815 cell line c, RMA cell line c, T2 cell line c, cancer cell line c

immortal cell line cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000019

A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
has super-classes
cell line cell c

immortalizing cell line transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001907

a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture
has super-classes
genetic transformation c
has_specified_input op some cell line cell c

immune complex formationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097281

The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus.
has super-classes
immunoglobulin mediated immune response c
has sub-classes
B cell epitope specific immune complex formation c

immune epitope assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110128

An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event
Source
IEDB
has super-classes
assay c
has sub-classes
MHC ligand assay c, assay measuring binding of a B cell epitope:antibody complex c, assay measuring binding of a T cell epitope:MHC:TCR complex c

immune epitope carrier rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110091

A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity.
Source
IEDB
has super-classes
role c

immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0006955

Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
has super-classes
response to stimulus c
has sub-classes
adaptive immune response c, histamine secretion mediated by immunoglobulin c

immune response assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000743

an assay with the objective to determine information about an immune response
is equivalent to
(has_specified_output op some measurement datum c and (is about op some immune response c)) and (achieves_planned_objective op some assay objective c)
has super-classes
assay c

immunizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110094

The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope.
Source
IEDB
Example
Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope).
is equivalent to
biological_process c and ((has participant op some epitope c and (part of op some immunogen c)) or (has participant op some epitope c and (derives from op some immunogen c))) and (has part op some epitope binding by adaptive immune receptor c) and (realizes op some immunogen role c) and (has participant op some (T cell c or B cell c) and (has function op some adaptive immune effector function c))
has super-classes
biological_process c
has sub-classes
Immunization in vivo c

Immunization in vitroc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110020

Process of administering an object playing the role of immunogen to a cell culture
Source
IEDB
has super-classes
material processing c
has part op some immunization c
has_specified_input op some cultured cell population c
has_specified_output op some cultured cell population c
achieves_planned_objective op some material transformation objective c

Immunization in vivoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110015

Process of administering an object playing the role of immunogen to a living organism
Source
IEDB
has super-classes
immunization c
has participant op some organism c
has sub-classes
Individual epitope immunization in vivo c

immuno staining assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001632

A detection of molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity.
Source
IEDB
Example
Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye.
has super-classes
detection of molecular label c
(realizes op some molecular label role c and (inheres in op some immunoglobulin complex, circulating c)) and (has_specified_input op some immunoglobulin complex, circulating c)
has sub-classes
immunohistochemistry c

immuno staining assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001652

A B cell epitope qualitative binding to antibody assay that uses an immuno staining assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some immuno staining assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c
has sub-classes
immunohistochemistry assay measuring binding of a B cell epitope:antibody complex c

immunoblot assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001978

An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with antibodies specific to the analyte molecules.
Source
IEDB
has super-classes
analyte assay c
(realizes op some function c and (inheres in op some gel electrophoresis system c)) and (has_specified_input op some gel electrophoresis system c)
(realizes op some analyte role c and (inheres in op some molecular entity c)) and (has_specified_input op some molecular entity c)
has part op some electrophoresis c
has sub-classes
western blot analysis c

immunoblot assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001650

A B cell epitope qualitative binding to antibody assay that uses an immunoblot assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some immunoblot assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

immunoblot scannerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001099

A device that is used for the imaging of immunoblots.
Source
PERSON: Erik Segerdell
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

immunogenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110023

a material entity bearing the immunogen role
Source
IEDB
is equivalent to
has role op some immunogen role c
has super-classes
material entity c

immunogen rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110082

any entity capable of eliciting an immune response when introduced to components of the immune system
Source
IEDB
has super-classes
role c

immunoglobulin binding to epitopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001702

a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR).
Source
IEDB
Example
Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus
has super-classes
binding c
epitope binding by adaptive immune receptor c
realizes op some disposition to be bound by an adaptive immune receptor c and (inheres in op some material entity c and (bound_to op some immunoglobulin complex, circulating c))
has participant op some immunoglobulin complex, circulating c
has participant op some material entity c and (bearer of op some disposition to be bound by an adaptive immune receptor c)
has sub-classes
B cell epitope specific immune complex formation c

immunoglobulin complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0019814

A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
has super-classes
protein complex c
has sub-classes
immunoglobulin complex, circulating c

immunoglobulin complex, circulatingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0042571

An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
has super-classes
immunoglobulin complex c
adaptive immune receptor c

immunoglobulin mediated histamine releasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001707

The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins.
Source
IEDB
has super-classes
biological_process c

immunoglobulin mediated immune responsec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0016064

An immune response mediated by immunoglobulins, whether cell-bound or in solution.
has super-classes
biological_process c
has sub-classes
immune complex formation c, immunoglobulin-mediated neutralization c

immunoglobulin-mediated neutralizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097282

The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin.
has super-classes
immunoglobulin mediated immune response c
has sub-classes
B cell epitope specific immunoglobulin-mediated neutralization c

immunohistochemistryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001986

An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section.
Source
IEDB
Example
Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques.
is equivalent to
immuno staining assay c and ((realizes op some evaluant role c and (inheres in op some specimen from organism c)) and (has_specified_input op some specimen from organism c)) and ((realizes op some molecular label role c and (inheres in op some material entity c)) and (has_specified_input op some material entity c))
has super-classes
immuno staining assay c

immunohistochemistry assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001998

A B cell epitope qualitative binding to antibody assay that uses an immunohistochemistry assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some immunohistochemistry c)
has super-classes
immuno staining assay measuring binding of a B cell epitope:antibody complex c

immunologic adjuvant rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000720

The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen.
Source
Vaccine Ontology, Wikipedia, OBI
Example
Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant
has super-classes
adjuvant role c
realized in op only immune response c

immunoprecipitationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000690

is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
Source
OBI plan and planned process branch
Example
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
has super-classes
material component separation c
has_specified_input op some immunoglobulin complex, circulating c
achieves_planned_objective op some material separation objective c
has sub-classes
chromatin immunoprecipitation c

immunoprecipitation assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001700

An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies.
Source
IEDB
Example
Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum.
is equivalent to
analyte assay c and ((realizes op some reagent role c and (inheres in op some immunoglobulin complex, circulating c)) and (has_specified_input op some immunoglobulin complex, circulating c)) and (has part op some immunoprecipitation c)
has super-classes
analyte assay c
has sub-classes
assay using chromatin immunoprecipitation c

immunoprecipitation assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001653

A B cell epitope qualitative binding to antibody assay that uses an immunoprecipitation assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some immunoprecipitation assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

imprinting designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001408

A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.
Source
MO_914 imprinting_design
has super-classes
study design c
has part op some molecular feature identification objective c

in container assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000978

an assay in which a measurement is made by observing entities located in a container.
has super-classes
assay c

in live cell assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000964

An assay in which a measurement is made by observing entities located in a live cell.
has super-classes
assay c

in live organism assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000966

An assay in which a measurement is made by observing entities located in an organism.
Example
Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
is equivalent to
assay c and (has participant op some located in op some organism c and (has quality op some alive c))
has super-classes
assay c

in situ hybridizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001686

is an assay using artificially induced nucleic hybridization to localize a specific DNA or RNA sequence in a portion or section of tissue
Source
PMID:9021518
Example
Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265
is equivalent to
(assay c and (has_specified_input op some labeled nucleic acid extract c) and (has_specified_output op some data item c and (is about op some macromolecule localization c))) and (achieves_planned_objective op some biological feature identification objective c)
has super-classes
assay c
has sub-classes
chromosome organization assay by fluorescence in situ hybridization c, transcript expression location detection by hybridization chain reaction c

in vitro assay measuring epitope specific proliferation of T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002071

A T cell epitope specific proliferation assay that is performed on cells in vitro.
Source
IEDB
has super-classes
biological activity assay measuring epitope specific proliferation of T cells c
has sub-classes
3H-thymidine assay measuring epitope specific proliferation of T cells c, BrdU assay measuring epitope specific proliferation of T cells c, carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells c

in vitro assay measuring epitope specific T cell killingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002062

A T cell epitope specific killing assay that uses an in vitro cell killing assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific T cell killing c and (has part op some in vitro cell killing assay c)
has super-classes
biological activity assay measuring epitope specific T cell killing c
has sub-classes
51 chromium assay measuring epitope specific T cell killing c

in vitro assay measuring T cell epitope specific suppressionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002074

T cell epitope dependent biological activity assay that detects suppression of an in vitro response.
Source
IEDB
has super-classes
assay measuring T cell epitope specific biological activity c

in vitro cell killing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000903

A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
Source
IEDB
Example
Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
is equivalent to
cell-cell killing assay c and ((realizes op some evaluant role c and (inheres in op some cultured cell population c)) and (has_specified_input op some cultured cell population c))
has super-classes
cell-cell killing assay c
has sub-classes
chromium release assay c

in vitro designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001285

A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
Source
MO_347 in_vitro_design
has super-classes
study design c

in vivo assay measuring B cell epitope specific disease exacerbationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001711

An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment.
Source
IEDB
is equivalent to
biological activity assay measuring B cell epitope specific in vivo activity c and (has part op some disease exacerbation in vivo intervention experiment c)
has super-classes
biological activity assay measuring B cell epitope specific in vivo activity c

in vivo assay measuring B cell epitope specific induction of hypersensitivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001694

An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions.
Source
IEDB
is equivalent to
biological activity assay measuring B cell epitope specific in vivo activity c and (has part op some in vivo intervention experiment c) and (has_specified_output op some information content entity c and (is about op some hypersensitivity c and (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
biological activity assay measuring B cell epitope specific in vivo activity c

in vivo assay measuring B cell epitope specific protection based on survivalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001696

A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on survival.
Source
IEDB
has super-classes
in vivo assay measuring B cell epitope specific protection from challenge c
has part op some protection from challenge in vivo intervention experiment c

in vivo assay measuring B cell epitope specific protection from challengec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001710

An efficacy of B cell epitope intervention experiment that uses a protection from challenge in vivo intervention experiment.
Source
IEDB
is equivalent to
biological activity assay measuring B cell epitope specific in vivo activity c and (has part op some protection from challenge in vivo intervention experiment c)
has super-classes
biological activity assay measuring B cell epitope specific in vivo activity c
has sub-classes
in vivo assay measuring B cell epitope specific protection based on survival c, in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden c, in vivo assay measuring B cell epitope specific protection from tumor challenge c

in vivo assay measuring B cell epitope specific protection from fertilityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001692

An efficacy of B cell epitope intervention experiment that uses a protection from challenge in vivo intervention experiment based on reduction of fertility.
Source
IEDB
has super-classes
biological activity assay measuring B cell epitope specific in vivo activity c
has part op some in vivo intervention experiment c
has_specified_input op some organism c

in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burdenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002051

A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on pathogen burden.
Source
IEDB
has super-classes
in vivo assay measuring B cell epitope specific protection from challenge c
has part op some protection from challenge in vivo intervention experiment c
has_specified_input op some material entity c and (has role op some pathogen role c)

in vivo assay measuring B cell epitope specific protection from tumor challengec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002052

A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on tumor burden.
Source
IEDB
has super-classes
in vivo assay measuring B cell epitope specific protection from challenge c
has part op some protection from challenge in vivo intervention experiment c
has_specified_input op some cancer cell line c

in vivo assay measuring B cell epitope specific tolerance inductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001693

An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment.
Source
IEDB
is equivalent to
biological activity assay measuring B cell epitope specific in vivo activity c and (has part op some tolerance induction intervention experiment c) and (has_specified_output op some information content entity c and (is about op some B cell tolerance induction c and (process is result of op some immunoglobulin binding to epitope c)))
has super-classes
biological activity assay measuring B cell epitope specific in vivo activity c

in vivo assay measuring B cell epitope specific treatment of diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001697

An efficacy of B cell epitope intervention experiment that detects a decrease in disease.
Source
IEDB
is equivalent to
biological activity assay measuring B cell epitope specific in vivo activity c and (has part op some treatment intervention experiment c)
has super-classes
biological activity assay measuring B cell epitope specific in vivo activity c

in vivo assay measuring epitope specific proliferation of T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002070

A T cell epitope specific proliferation assay that is performed in vivo.
Source
IEDB
has super-classes
biological activity assay measuring epitope specific proliferation of T cells c

in vivo assay measuring epitope specific T cell killingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001392

A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific T cell killing c and (has part op some in vivo cell killing assay c)
has super-classes
biological activity assay measuring epitope specific T cell killing c

in vivo assay measuring T cell epitope specific disease exacerbationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001467

An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment.
Source
IEDB
is equivalent to
biological activity assay measuring T cell epitope specific in vivo activity c and (has part op some disease exacerbation in vivo intervention experiment c)
has super-classes
biological activity assay measuring T cell epitope specific in vivo activity c

in vivo assay measuring T cell epitope specific protection based on survivalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001492

A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on survival.
Source
IEDB
is equivalent to
in vivo assay measuring T cell epitope specific protection from challenge c and (has part op some epitope protection experiment based on survival c)
has super-classes
in vivo assay measuring T cell epitope specific protection from challenge c

in vivo assay measuring T cell epitope specific protection from challengec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002073

An efficacy of T cell epitope intervention experiment that uses a protection from challenge in vivo intervention experiment.
Source
IEDB
is equivalent to
biological activity assay measuring T cell epitope specific in vivo activity c and (has part op some protection from challenge in vivo intervention experiment c)
has super-classes
biological activity assay measuring T cell epitope specific in vivo activity c
has sub-classes
in vivo assay measuring T cell epitope specific protection based on survival c, in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden c, in vivo assay measuring T cell epitope specific protection from tumor challenge c

in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burdenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001475

A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on pathogen burden.
Source
IEDB
is equivalent to
in vivo assay measuring T cell epitope specific protection from challenge c and (has part op some protection from challenge in vivo intervention experiment c) and (has_specified_input op some material entity c and (has role op some pathogen role c))
has super-classes
in vivo assay measuring T cell epitope specific protection from challenge c

in vivo assay measuring T cell epitope specific protection from tumor challengec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001473

A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on tumor burden.
Source
IEDB
is equivalent to
in vivo assay measuring T cell epitope specific protection from challenge c and (has part op some protection from challenge in vivo intervention experiment c) and (has_specified_input op some cancer cell line c)
has super-classes
in vivo assay measuring T cell epitope specific protection from challenge c

in vivo assay measuring T cell epitope specific tolerance inductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001324

An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment.
Source
IEDB
is equivalent to
biological activity assay measuring T cell epitope specific in vivo activity c and (has part op some tolerance induction intervention experiment c) and (has_specified_output op some information content entity c and (is about op some T cell tolerance induction c and (process is result of op some MHC:epitope complex binding to TCR c)))
has super-classes
biological activity assay measuring T cell epitope specific in vivo activity c

in vivo assay measuring T cell epitope specific treatment of diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001507

An efficacy of T cell epitope intervention experiment that detects a decrease in disease.
Source
IEDB
is equivalent to
biological activity assay measuring T cell epitope specific in vivo activity c and (has part op some treatment intervention experiment c)
has super-classes
biological activity assay measuring T cell epitope specific in vivo activity c

in vivo cell killing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000883

A cell killing assay that measures if and how many target cells are killed within an organism.
Source
IEDB
Example
Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells.
is equivalent to
cell-cell killing assay c and ((realizes op some evaluant role c and (inheres in op some organism c)) and (has_specified_input op some organism c))
has super-classes
cell-cell killing assay c

in vivo designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001199

A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
Source
MO_454 in_vivo_design
has super-classes
study design c

in vivo intervention experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001980

An assay in which the effect of a targeted process (the intervention) on an organism is tested.
Source
IEDB
Example
Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival.
has super-classes
assay c
(realizes op some evaluant role c and (inheres in op some organism c)) and (has_specified_input op some organism c)
has sub-classes
disease exacerbation in vivo intervention experiment c, protection from challenge in vivo intervention experiment c, tolerance induction intervention experiment c, treatment intervention experiment c

in vivo skin test assay measuring T cell epitope specific type IV hypersensitivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001348

An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity.
Source
IEDB
is equivalent to
biological activity assay measuring T cell epitope specific in vivo activity c and (has_specified_output op some information content entity c and (is about op some type IV hypersensitivity c and (process is result of op some MHC:epitope complex binding to TCR c)))
has super-classes
biological activity assay measuring T cell epitope specific in vivo activity c

in-line filterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000538

A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity.
Source
WEB:<http://www.appliedporous.com/frits-chromatography.htm>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123
has super-classes
chromatography detector filter c

inclusion criteriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500027

an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
Source
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
Example
PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
has super-classes
eligibility criterion c

incubatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000136

a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
Source
http://www.medterms.com/script/main/art.asp?articlekey=18426
Example
Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
has super-classes
physical store c
has function op some environment control function c
has sub-classes
hybridization oven c

incubator shakerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001076

An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures).
Source
PERSON: Erik Segerdell
has super-classes
physical store c
has function op some contain function c
has function op some mechanical function c
has function op some environment control function c

independent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000004

A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
has super-classes
continuant c
has sub-classes
immaterial entity c, material entity c
is in domain of
derives from op, has role op
is in range of
derives from op, occurs in op
is disjoint with
specifically dependent continuant c, generically dependent continuant c

indirect detection probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000640

An NMR probe designed to allow the indirect detection of acquisition nuclei.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281
has super-classes
NMR probe c

Individual epitope immunization in vivoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001176

An immunization in which an individual epitope is administered into a host organism.
Example
Injection of a peptide T cell epitope into a mouse
has super-classes
Immunization in vivo c

individual genetic characteristics comparison designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001448

A study design where genotype, haplotype, or other individual genetic characteristics are compared.
Source
MO_527 individual_genetic_characteristics_design
has super-classes
study design c
has part op some biological feature identification objective c
has part op some study design independent variable c and (is about op some genetic characteristics information c)

individual organism identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001141

a CRID symbol used to distinguish one individual organism from another.
Source
MO_169 Individual
has super-classes
centrally registered identifier symbol c
denotes op only organism c

individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002043

A cross-linking immunoprecipitation high-throughput sequencing assay to identify protein-RNA interactions by using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes.
Source
Huppertz et al., (February 2014). "iCLIP: protein-RNA interactions at nucleotide resolution.". Methods (San Diego, Calif.) 65 (3): 274-87. doi:10.1016/j.ymeth.2013.10.011
Example
König et al., (18 January 2012). "Protein-RNA interactions: new genomic technologies and perspectives". Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141
has super-classes
cross-linking immunoprecipitation high-throughput sequencing assay c
has sub-classes
enhanced cross-linking immunoprecipitation high-throughput sequencing assay c

induced hemagglutinationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000906

The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
Source
WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination
has super-classes
material processing c
has_specified_input op some erythrocyte c

induced mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001154

a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation.
Source
MO_564 induced_mutation
has super-classes
genetic transformation c

inductive reasoningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000343

a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns.
Source
wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning
Example
Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer.
has super-classes
drawing a conclusion based on data c

infectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IDO_0000586

A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
has super-classes
material entity c

infection processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110021

the detrimental process in which an infectious agent colonizes or replicates in a host environment
Source
IEDB
has super-classes
pathologic process c
realizes op some disposition to infect an organism c
has participant op some infection c

infectious agentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000925

is a material entity bearing the disposition to infect an organism
Source
IEDB
is equivalent to
bearer of op some disposition to infect an organism c
has super-classes
organism c

infectious agent detection assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001187

An assay in which the presence or amount of an infectious agent in an input material is detected in an evaluant
Example
Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers.
has super-classes
assay c

infectious diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110040

is a disease caused by an infectious agent
Source
IEDB
has super-classes
disease c

inFlux Analyzerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400055

The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells.
Source
http://www.cytopeia.com/analyzer.htm
has super-classes
flow cytometer analyzer c

Influx Cell Sorterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400056

A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells.
Source
http://www.cytopeia.com/sorter.htm
Example
Influx Cell Sorter at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

information acquisitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600013

An acquisition in which possession of information is gained.
Source
OBI branch derived
Example
Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC
has super-classes
acquisition c
has_specified_output op some information content entity c
is disjoint with
assay c, data transformation c

information carrierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000015

A quality of an information bearer that imparts the information content
Source
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
Example
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
is equivalent to
quality c and (concretizes op some information content entity c)
has super-classes
quality c

information content entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000030

A generically dependent continuant that is about some thing.
Source
OBI_0000142
Example
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has super-classes
generically dependent continuant c
is about op some entity c
has sub-classes
analytical cytology data file c, centrally registered identifier c, clinical history c, conclusion based on data c, curated information c, data item c, datum label c, directive information entity c, document c, document part c, eMedical record c, eSource document c, electronic case report form c, electronic case report tabulation c, email address c, figure c, fluorescence compensation matrix c, list-mode data file c, narrative object c, predicted value c, record of missing knowledge c, sequence feature annotation c, symbol c, testable hypothesis c, textual entity c, validated information c, value specification c
is in domain of
has value specification op, is about op

information processor functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000392

An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
has super-classes
function c
has part op some measure function c
has part op some consume data function c
has sub-classes
display function c, signal conversion function c

informed consent processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000810

A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
Source
http://clinicaltrials.gov/ct2/info/glossary#informed
has super-classes
planned process c
has_specified_input op some Homo sapiens c
has participant op some has role op some investigation agent role c

informing investigator of subject study armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000804

A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
has super-classes
planned process c
(has_specified_input op some denotes op some bearer of op some participant under investigation role c) and (has participant op some has role op some investigation agent role c)

informing subject of study armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000842

A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
has super-classes
planned process c
(part of op some informed consent process c) and (has participant op some has role op some participant under investigation role c)

infrared image acquisition devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001078

An image acquisition device that is responsive to an infrared emissive target within a given field of view.
Source
United States Patent 4107530
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

injectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000426

injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
Source
OBI Biomaterial
Example
Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
is equivalent to
(realizes op some material to be added role c) and (realizes op some function c and (inheres in op some syringe c))
has super-classes
adding a material entity into a target c
achieves_planned_objective op some adding material objective c
has sub-classes
injection into organ section c, intradermal injection c, intramuscular injection c, intraperitoneal injection c, intravenous injection c, subcutaneous injection c

injection functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0005246

The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc.
Source
adapted from WEB: http://www.dictionary.net/injection
has super-classes
function c

injection into organ sectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000431

A process in which an input substance is injected into a organ section.
Example
Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology
is equivalent to
(realizes op some material to be added role c) and (realizes op some function c and (inheres in op some syringe c)) and (realizes op some target of material addition role c and (role of op some organ section c))
has super-classes
injection c
achieves_planned_objective op some adding material objective c

injector lubricantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000511

A lubricant used in liquid chromatography that eases sample injector penetration.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118
has super-classes
chromatography consumable c

injury designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001374

A study design in which the response of an organism(s) to injury or damage is studied.
Source
MO_726 injury_design
has super-classes
study design c
has part op some organism feature identification objective c

inline probing RNA structure mappingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001039

is a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses intromolecular reactivity to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:10573122 and PMID: 18369975
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some ribonucleic acid c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

innate behavior designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001202

A study design in which the innate behavior of the organism is examined, e.g. path finding in bees.
Source
MO_355 innate_behavior_design
has super-classes
study design c
has part op some organism feature identification objective c

institution listc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000322

part of a document that has parts that are institution identifications associated with the authors of the document
Example
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
has super-classes
document part c
has part op some institutional identification c

institutional identificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000303

A textual entity intended to identify a particular institution
Example
University of Colorado Denver School of Medicine
has super-classes
textual entity c

Insulin resistancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/HP_0000855

Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.
has super-classes
disposition c

integer numeralc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000031

a numeral that denotes an integer
has super-classes
numeral c

intentional overdosingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302898

intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death
Source
OBI Biomaterial
Example
In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment. J Neurooncol. 1994;22(3):209-20. PMID: 7760097
has super-classes
animal euthanization c
has_specified_input op some molecular entity c

inter-rater reliability objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200091

a data transformation objective of determining the concordance or agreement between human judges.
Source
http://en.wikipedia.org/wiki/Inter-rater_reliability
Example
A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation.
has super-classes
data transformation objective c

interferon-beta productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032608

The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interferon-beta production by T cells c

interferon-gamma productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032609

The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
has super-classes
cytokine production c
has sub-classes
epitope specific IFN-g release by T cells c

interleukin-1 alpha productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032610

The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
interleukin-1 production c
has sub-classes
epitope specific interleukin-1 alpha production by T cells c

interleukin-1 beta productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032611

The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
interleukin-1 production c
has sub-classes
epitope specific IL-1b release by T cells c

interleukin-1 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032612

The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
interleukin-1 alpha production c, interleukin-1 beta production c

interleukin-10 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032613

The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-10 release by T cells c

interleukin-11 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032614

The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

interleukin-12 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032615

The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-12 release by T cells c

interleukin-13 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032616

The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-13 release by T cells c

interleukin-14 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032617

The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

interleukin-15 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032618

The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-15 production by T cells c

interleukin-16 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032619

The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-16 production by T cells c

interleukin-17 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032620

The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-17 release by T cells c, interleukin-17A production c, interleukin-17F production c

interleukin-17A productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097087

The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
interleukin-17 production c
has sub-classes
epitope specific interleukin-17A production by T cells c

interleukin-17F productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0097088

The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
interleukin-17 production c
has sub-classes
epitope specific interleukin-17F production by T cells c

interleukin-18 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032621

The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-18 release by T cells c

interleukin-19 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032622

The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

interleukin-2 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032623

The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-2 release by T cells c

interleukin-20 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032624

The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

interleukin-21 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032625

The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-21 production by T cells c

interleukin-22 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032626

The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-22 production by T cells c

interleukin-23 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032627

The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-23 production by T cells c

interleukin-24 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032628

The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

interleukin-25 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032629

The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

interleukin-26 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032630

The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

interleukin-27 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032631

The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-27 production by T cells c

interleukin-3 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032632

The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-3 production by T cells c

interleukin-4 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032633

The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-4 release by T cells c

interleukin-5 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032634

The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-5 release by T cells c

interleukin-6 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032635

The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific IL-6 release by T cells c

interleukin-7 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032636

The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-7 production by T cells c

interleukin-8 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032637

The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-8 production by T cells c

interleukin-9 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032638

The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific interleukin-9 production by T cells c

interquartile-range calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200122

The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data.
Source
PERSON: Monnie McGee
has super-classes
spread calculation data transformation c
descriptive statistical calculation data transformation c
achieves_planned_objective op some descriptive statistical calculation objective c
achieves_planned_objective op some spread calculation objective c

interrogation_pointc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400059

Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point.
Source
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11
Example
Interrogation point in BD FACS Calibur
has super-classes
site c

intervention designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000115

An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
Source
OBI branch derived
Example
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
is equivalent to
study design c and (has part op some study design independent variable c and (is about op some study intervention c))
has super-classes
study design c
has sub-classes
compound treatment design c, genetic modification design c, growth condition intervention design c, post-transcriptional modification design c, randomized complete block design c, repeated measure design c, sequential design c, stimulus or stress design c

intra cellular electrophysiology recordingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000447

An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular
Source
PERSON: Frank Gibson
has super-classes
assay c
has_specified_output op some measurement datum c and (is about op some ion channel activity c)
achieves_planned_objective op some assay objective c

intra subgraph connectivity calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200145

A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph.
Source
PERSON: Richard Scheuermann
has super-classes
network subgraph quality calculation c

intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001768

An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells c

intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001370

An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells c

intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001437

An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells c

intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001750

An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells c

intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001303

An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells c

intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001749

An assay of epitope specific interferon-beta production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-beta production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interferon-beta production by T cells c

intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110172

An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-gamma production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interferon-gamma production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001744

An assay of epitope specific interleukin-1 alpha production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001841

An assay of epitope specific interleukin-1 beta production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-1 beta production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110177

An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-10 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-10 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001466

An assay of epitope specific interleukin-12 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-12 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-12 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001309

An assay of epitope specific interleukin-13 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-13 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-13 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001845

An assay of epitope specific interleukin-15 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-15 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-15 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001839

An assay of epitope specific interleukin-16 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-16 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-16 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110178

An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-17 production by T cells c
has sub-classes
intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells c, intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001589

A T cell epitope specific interleukin-17A production assay that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17A production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-17A production by T cells c
intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001562

A T cell epitope specific interleukin-17F production assay that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-17F production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-17F production by T cells c
intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001824

An assay of epitope specific interleukin-18 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-18 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-18 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110173

An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-2 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-2 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001342

An assay of epitope specific interleukin-21 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-21 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-21 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001496

An assay of epitope specific interleukin-22 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-22 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-22 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001812

An assay of epitope specific interleukin-23 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-23 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-23 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001806

An assay of epitope specific interleukin-27 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-27 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-27 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001376

An assay of epitope specific interleukin-3 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-3 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-3 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110175

An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-4 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-4 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001299

An assay of epitope specific interleukin-5 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-5 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-5 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001240

An assay of epitope specific interleukin-6 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-6 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-6 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001805

An assay of epitope specific interleukin-7 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-7 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-7 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001609

An assay of epitope specific interleukin-8 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-8 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-8 production by T cells c

intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001798

An assay of epitope specific interleukin-9 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring interleukin-9 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring interleukin-9 production by T cells c

intracellular cytokine staining assay measuring epitope specific IP-10 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001796

An assay of epitope specific IP-10 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific IP-10 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific IP-10 production by T cells c

intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001453

An assay of epitope specific lymphotoxin A production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific lymphotoxin A production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific lymphotoxin A production by T cells c
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c

intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001545

An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells c

intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001785

An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells c

intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001783

An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells c

intracellular cytokine staining assay measuring epitope specific RANTES production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001789

An assay of epitope specific RANTES production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific RANTES production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific RANTES production by T cells c

intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001482

An assay of epitope specifictransforming growth factor-beta production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells c

intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001552

A T cell epitope specific tumor necrosis factor (ligand) superfamily member 11 production assay that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells c and (has part op some flow cytometry assay c)
has super-classes
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells c

intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110174

A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c and (has part op some flow cytometry assay c)
has super-classes
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
biological activity assay measuring epitope specific tumor necrosis factor production by T cells c

intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001385

An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells c
has sub-classes
intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells c, intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells c, intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells c

intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001770

An assay of epitope specific vascular endothelial growth factor production by T cells that uses an intracellular cytokine staining assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells c

intracellular material detection assay measuring epitope specific granulysin release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001664

A T cell epitope specific granulysin release assay that uses an intracellular material detection by flow cytometry assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granulysin release by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific granulysin release by T cells c

intracellular material detection assay measuring epitope specific granzyme A release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001660

A T cell epitope specific granzyme A release assay that uses an intracellular material detection by flow cytometry assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granzyme A release by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific granzyme A release by T cells c

intracellular material detection assay measuring epitope specific perforin releasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001215

A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific perforin release by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific perforin release by T cells c

intracellular material detection measuring epitope specific granzyme B release by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001423

A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific granzyme B release by T cells c and (has part op some flow cytometry assay c)
has super-classes
biological activity assay measuring epitope specific granzyme B release by T cells c

intradermal injectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000942

is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe
is equivalent to
(realizes op some material to be added role c) and (realizes op some function c and (inheres in op some syringe c)) and (realizes op some target of material addition role c and (role of op some dermis c))
has super-classes
injection c
administering substance in vivo c
achieves_planned_objective op some adding material objective c

intramuscular injectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000934

is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe
is equivalent to
(realizes op some material to be added role c) and (realizes op some function c and (inheres in op some syringe c)) and (realizes op some target of material addition role c and (role of op some skeletal muscle tissue c))
has super-classes
injection c
administering substance in vivo c
achieves_planned_objective op some adding material objective c

intranasal mucosal administrationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000983

The administration of a substance into the intranasal mucosis of an organism
is equivalent to
(realizes op some material to be added role c) and (realizes op some target of material addition role c and (role of op some mucosa of nasopharynx c))
has super-classes
administering substance in vivo c
achieves_planned_objective op some adding material objective c

intraperitoneal administrationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000429

The administration of a substance into the peritoneum of an organism
Example
Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h
is equivalent to
(realizes op some material to be added role c) and (realizes op some target of material addition role c and (role of op some peritoneum c))
has super-classes
administering substance in vivo c
achieves_planned_objective op some adding material objective c
has sub-classes
intraperitoneal injection c

intraperitoneal injectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000281

is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe
is equivalent to
(realizes op some material to be added role c) and (realizes op some function c and (inheres in op some syringe c)) and (realizes op some target of material addition role c and (role of op some peritoneum c))
has super-classes
injection c
intraperitoneal administration c
achieves_planned_objective op some adding material objective c

intravenous injectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000994

is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe
is equivalent to
(realizes op some material to be added role c) and (realizes op some function c and (inheres in op some syringe c)) and (realizes op some target of material addition role c and (role of op some vein c))
has super-classes
injection c
administering substance in vivo c
achieves_planned_objective op some adding material objective c

introduction to a publication about an investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000316

A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
Example
Section labelled 'introduction' of a typical scientific journal article
has super-classes
document part c
is about op some objective specification c

investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000066

a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Source
OBI branch derived
Example
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has super-classes
planned process c
has part op some documenting c
has part op some drawing a conclusion based on data c
has part op some study design execution c
has part op some planning c and (has_specified_output op some study design c)
has sub-classes
hypothesis driven investigation c, hypothesis generating investigation c

investigation agent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000202

A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Source
OBI
Example
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
is equivalent to
role c and (inheres in op some bearer of op some concretizes op some objective_achieved_by op some part of op some investigation c)
has super-classes
role c
realized in op only investigation c
has sub-classes
reporting party role c, responsible party role c, specimen collector role c, worker role c

investigation assay specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001896

A plan specification which indicates the assay type used to obtain data.
Source
NIAID GSCID-BRC metadata working group
Example
Some examples of Project Method are Sequence, Array, Mass Spectrometry
has super-classes
plan specification c
part of op some study design c
is about op some assay c

investigation descriptionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001615

A textual entity that describes an investigation.
Source
NIAID GSCID-BRC metadata working group
has super-classes
textual entity c
is about op some investigation c

investigation identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001628

A CRID symbol used to identify an investigation.
Source
NIAID GSCID-BRC metadata working group
has super-classes
centrally registered identifier symbol c
denotes op only investigation c

investigation results reportc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000218

An investigation report is a report on the results of an investigation.
Source
group:OBI
has super-classes
report c

investigation titlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001622

A textual entity that denotes an investigation.
Source
NIAID GSCID-BRC metadata working group
has super-classes
textual entity c
denotes op some investigation c

Ion 314 Chip v2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001974

An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb.
Source
http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html
has super-classes
ion semiconductor chip c

Ion 316 Chip v2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001971

An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb.
Source
http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html
has super-classes
ion semiconductor chip c

Ion 318 Chip v2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001972

An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb.
Source
http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html
has super-classes
ion semiconductor chip c

ion channel activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0005216

Catalysis of facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
has super-classes
cellular process c

ion detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000364

An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q.
Source
http://en.wikipedia.org/wiki/Mass_spectrometry#Detector
Example
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
has super-classes
measurement device c
has function op some measure function c
has sub-classes
ion semiconductor chip c

ion exchange columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000560

An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105
has super-classes
chromatography column c
has sub-classes
anion exchange column c, cation exchange column c

ion laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400060

An ion laser is a gas laser which uses an ionized gas as its lasing medium.
Source
John Quinn
http://en.wikipedia.org/wiki/Ion_laser
Example
2 Watt Lexel 88 Argon Ion laser
has super-classes
gas laser c
has sub-classes
argon ion laser c, helium neon ion laser c, krypton ion laser c, mixed argon-krypton gas laser c

ion semiconductor chipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001973

An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface.
Source
http://www.thefreedictionary.com/Semiconductor+chip
has super-classes
ion detector c
has sub-classes
Ion 314 Chip v2 c, Ion 316 Chip v2 c, Ion 318 Chip v2 c

ion sourcec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000361

An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))).
Source
http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source
Example
The ion source of a Voyager-DE??? STR Biospectrometry Workstation
has super-classes
device c
has function op some ionization function c

ionization functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000385

An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
Source
http://en.wikipedia.org/wiki/Ionization
Example
The ion source in amass spectrometer
has super-classes
function c

ionize processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000373

a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation.
Example
Electrospray ionization in mass spectrometry
has super-classes
material processing c
realizes op some ionization function c
achieves_planned_objective op some material transformation objective c
has participant op some continuant c

IP-10 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071612

The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific IP-10 production by T cells c

irradiationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302889

irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves
Source
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
Example
PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
has super-classes
material processing c
has_specified_input op some material entity c
achieves_planned_objective op some material transformation objective c
has participant op some light source c

isocratic pump systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000556

A pump system optimized for isocratic chromatography.
Source
WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049
has super-classes
chromatography pump system c

isoelectric focusing devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000389

An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated.
Source
sep:00097
has super-classes
physical store c
bearer of op some device setting c
has function op some contain function c
has function op some transfer function c
has function op some environment control function c

isolation of adherent cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000540

a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells.
has super-classes
isolation of cell population c
has_specified_input op some cultured cell population c
has_specified_output op some cultured cell population c

isolation of cell culture supernatantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600029

a protocol which results in the separation of supernatant material from a cell culture
Source
OBI branch derived
Example
Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube.
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c

isolation of cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000512

a process in which a population of cells with certain characteristics is isolated from a larger population
Example
removing CD4+ cells from PBMCs using magnetic beads.
has super-classes
material component separation c
has_specified_input op some cultured cell population c
has_specified_output op some cultured cell population c
achieves_planned_objective op some separation into different composition objective c
has sub-classes
isolation of PBMCs c, isolation of adherent cells c

isolation of PBMCsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000548

a process in which cells with a single nucleus are isolated from a blood sample
Source
wiki http://en.wikipedia.org/wiki/PBMC
Example
cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs.
has super-classes
isolation of cell population c
has_specified_input op some blood c
has_specified_output op some cultured cell population c
achieves_planned_objective op some separation into different composition objective c

jackknifing methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200034

Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method
Source
http://en.wikipedia.org/wiki/Resampling_%28statistics%29
Example
simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure
has super-classes
statistical model validation c
achieves_planned_objective op some cross validation objective c

JAWS II cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110033

A cell line derived from mouse dendritic cells.
Source
IEDB
http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology
has super-classes
immortal cell line c

JEOL CapNMR probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000635

The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility.
Source
WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233
has super-classes
JEOL NMR probe c

JEOL ECA NMR spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000641

The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
Source
WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228
has super-classes
JEOL NMR instrument c

JEOL ECX NMR spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000625

The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
Source
WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227
has super-classes
JEOL NMR instrument c

JEOL NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000600

An NMR instrument that is manufactured by JEOL.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226
has super-classes
NMR instrument c
has sub-classes
JEOL ECA NMR spectrometer c, JEOL ECX NMR spectrometer c

JEOL NMR probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000529

An NMR probe that is manufactured by JEOL.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232
has super-classes
NMR probe c
has sub-classes
JEOL CapNMR probe c

jet_in_air_flow_chamberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400061

A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air.
Source
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
Example
Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter
has super-classes
site c

journal articlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000013

a report that is published in a journal
Source
OBI_0000159
group:OBI
Example
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
has super-classes
report c

Jurkat cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110035

A cell line derived from human T cells.
Source
IEDB
http://www.biotech.ist.unige.it/cldb/cl5296.html
has super-classes
immortal cell line c

JY cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110036

The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia)
Source
IEDB
has super-classes
immortal cell line c

K-fold cross validation methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200032

K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used
Source
Tina Boussard
has super-classes
statistical model validation c
achieves_planned_objective op some cross validation objective c

k-means clusteringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200041

A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
Source
WEB: http://en.wikipedia.org/wiki/K-means
has super-classes
partitioning data transformation c
class discovery data transformation c
(has_specified_output op some clustered data set c) and (achieves_planned_objective op some class discovery objective c)
achieves_planned_objective op some partitioning objective c
has members
GenePattern k-means clustering ni

k-nearest neighborsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000727

A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
Source
PERSON: James Malone
has super-classes
partitioning data transformation c
class discovery data transformation c
(has_specified_output op some clustered data set c) and (achieves_planned_objective op some class discovery objective c)
achieves_planned_objective op some partitioning objective c
has members
GenePattern k-nearest neighbors ni

Kaplan Meierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200088

a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored)
Source
http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator
has super-classes
survival analysis data transformation c
achieves_planned_objective op some survival analysis objective c

kethoxal structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001013

is a single-nucleotide-resolution nucleic acid structure mapping assay which uses kethoxal as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
single nucleotide resolution mapping assay using Kethoxal probe
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some 1,1-dihydroxy-3-ethoxy-2-butanone c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

killer cell immunoglobulin-like receptor typing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002121

A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined.
Source
http://www.ncbi.nlm.nih.gov/pubmed/21239231
Example
DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself.
has super-classes
genotyping assay c

killingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600006

A protocol application in which an organism is intentionally put to death
Source
CEBS, Biomaterial_branch
Example
Terminal sacrifice of animals by cervical dislocation at the end of an investigation.
has super-classes
material processing c
has_specified_input op some organism c and (has quality op some alive c)
has_specified_output op some organism c and (has quality op some dead c)
achieves_planned_objective op some material transformation objective c
has sub-classes
animal euthanization c, cell lysis c

krypton ion laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400062

A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however.
Source
John Quinn
Example
Lexel 95L krypton laser
has super-classes
ion laser c

kurtosis calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200124

A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html
Source
WEB: http://davidmlane.com/hyperstat/A53638.html
has super-classes
spread calculation data transformation c
descriptive statistical calculation data transformation c
achieves_planned_objective op some descriptive statistical calculation objective c
achieves_planned_objective op some spread calculation objective c

L cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110099

A cell line derived from mouse fibroblasts.
Source
IEDB
http://www.biotech.ist.unige.it/cldb/cl3075.html
has super-classes
immortal cell line c

labeled DNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000908

a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
Source
Group: OBI group
has super-classes
labeled nucleic acid extract c
(is_specified_output_of op some addition of molecular label c and (has_specified_input op some DNA extract c)) and (has role op some specimen role c)
has grain op some deoxyribonucleic acid c

labeled nucleic acid extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001143

a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
Source
MO_221 labeledExtract
has super-classes
labeled specimen c
(is_specified_output_of op some addition of molecular label c and (has_specified_input op some nucleic acid extract c)) and (has role op some specimen role c)
has grain op some nucleic acid c
has sub-classes
labeled DNA extract c, labeled RNA extract c

labeled oligonucleotidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000839

a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide
Example
has super-classes
molecular-labeled material c
has part op some molecular label c
is_specified_output_of op some addition of molecular label c

labeled RNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000921

a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
Source
Group: OBI group
has super-classes
labeled nucleic acid extract c
(is_specified_output_of op some addition of molecular label c and (has_specified_input op some RNA extract c)) and (has role op some specimen role c)
has grain op some ribonucleic acid c

labeled specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000924

A specimen that has been modified in order to be able to detect it in future experiments
is equivalent to
specimen c and (has part op some molecular label c) and (is_specified_output_of op some addition of molecular label c)
has super-classes
processed specimen c
molecular-labeled material c
has sub-classes
labeled nucleic acid extract c

laboratory animal carec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000708

a process that realizes an animal care protocol that specifies how animals are kept and maintained
is equivalent to
realizes op some concretizes op some animal care protocol c
has super-classes
planned process c
has_specified_output op some organism c and (located in op some site c)
has sub-classes
rodent care c

LactoScope C4c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400063

A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy.
Source
http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm
Example
LactoScope C4 Automatic Economical
has super-classes
spectrophotometer c

laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400064

A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer.
Source
John Quinn
http://en.wikipedia.org/wiki/Laser
Example
A laser is the most common way to irradiate a cell in a flow cytometer.
has super-classes
light source c
has sub-classes
diode laser c, dye laser c, gas laser c, solid state laser c

laser capture microdissection microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001096

A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue.
Source
http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine
has super-classes
microscope c
has function op some measure function c

laser scanning confocal microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001125

A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen.
Source
http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy
has super-classes
confocal microscope c
has function op some measure function c

lateral toc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001193

A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity.
has super-classes
relational spatial quality c

latin square designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500011

Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
Source
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
Example
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
has super-classes
randomized complete block design c

latitude coordinate measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001620

A measurement datum that is the measure of the latitude coordinate of a site.
Source
NIAID GSCID-BRC metadata working group
has super-classes
measurement datum c

lavagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600044

A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
Source
OBI branch derived
Example
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
has super-classes
collecting specimen from organism c
material component separation c
achieves_planned_objective op some material separation objective c

Lead structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001020

a single-nucleotide-resolution nucleic acid structure mapping assay which uses lead as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:2686708
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some lead(0) c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

lead(0)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_27889

An elemental lead that has formula Pb.
has super-classes
molecular entity c

leave one out cross validation methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200033

is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
Example
The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
has super-classes
statistical model validation c
achieves_planned_objective op some cross validation objective c
has members
GenePattern LOOCV ni

left cerebral hemispherec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002812

A cerebral hemisphere that is in the left side of a brain.
has super-classes
material anatomical entity c

left handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0002202

Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
has super-classes
handedness c

left side ofc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001792

A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity.
has super-classes
relational spatial quality c

lengthc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000122

A 1-D extent quality which is equal to the distance between two points.
has super-classes
quality c

length measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000408

A scalar measurement datum that is the result of measurement of length quality
has super-classes
scalar measurement datum c
has measurement unit label op some length unit c
is quality measurement of op some length c

length unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000001

A unit which is a standard measure of the distance between two points.
has super-classes
measurement unit label c
is in range of
has coordinate unit label op
has members
angstrom ni, centimeter ni, meter ni, micrometer ni, millimeter ni, nanometer ni

Li-Cor 4300 DNA Analysis Systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000710

is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
Source
OBI and Li-Cor
has super-classes
DNA sequencer c
is_manufactured_by op value Li-Cor

library preparationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000711

is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
Example
PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120.
has super-classes
material processing c
has_specified_input op some deoxyribonucleic acid c or double-stranded DNA c
has_specified_output op some cDNA library c or paired-end library c or single fragment library c or phage display library c
achieves_planned_objective op some material transformation objective c
has sub-classes
SAGE ditag library preparation c, paired-end library preparation c

life cycle stagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000105

A spatiotemporal region encompassing some part of the life cycle of an organism.
has super-classes
biological_process c

light emission devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001032

a device which has a function to emit light.
Source
OBI
Example
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
is equivalent to
has function op some light emission function c
has super-classes
device c
has sub-classes
light source c, molecular crosslinker c

light emission functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000367

A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
has super-classes
excitation function c

light sourcec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400065

A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
has super-classes
light emission device c
has function op some light emission function c
has sub-classes
arc lamp c, laser c, two-photon laser/detector c

Likelihood-ratio testc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000861

Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models.
has super-classes
data transformation c

line graphc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000573

A line graph is a type of graph created by connecting a series of data points together with a line.
Source
GROUP:OBI
WEB: http://en.wikipedia.org/wiki/Line_chart
has super-classes
graph c
has sub-classes
dose response curve c, survival curve c

linear amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001494

An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
Source
MO_997 linear_amplification
Example
An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
has super-classes
enzymatic amplification c

linear discriminant functional analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200101

Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective.
Source
PERSON: Tina Hernandez-Boussard
has super-classes
class prediction data transformation c
discriminant analysis c
class discovery data transformation c
(has_specified_output op some classified data set c) and (achieves_planned_objective op some class prediction objective c)
has_specified_output op some clustered data set c

linlog transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200021

A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm.
Source
PMID: 16646782
Example
This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

liquid chromatography autosamplerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000494

Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061
has super-classes
chromatography instrument c
has sub-classes
dual loop autosampler c, preparative autosampler c

liquid chromatography columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000603

A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227
has super-classes
chromatography column c

liquid chromatography instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001139

A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
Source
PERSON: Matthew Brush
has super-classes
chromatography device c
has sub-classes
high performance liquid chromatography instrument c

liquid chromatography mass spectrometry platformc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000051

A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.
Source
OBI Instrument branch
has super-classes
measurement device c
material separation device c
has part op some chromatography device c
has part op some mass spectrometer c
has function op some material separation function c
has function op some measure function c

liquid chromatography valvec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000528

A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent.
Source
WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110
has super-classes
chromatography device c

liquid extraction robotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001097

A liquid handling device that provides automatic liquid extraction.
Source
PERSON: Erik Segerdell
has super-classes
liquid handler c
has function op some mechanical function c

liquid filter functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000381

A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture
has super-classes
filter function c

liquid handlerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400112

a device that is used for automated liquid transfer and handling.
Source
MO_868 liquid_handler
Example
Beckman BioMek 2000
has super-classes
device c
has function op some transfer function c
has sub-classes
liquid extraction robot c

liquid NMR probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000559

An NMR probe that is designed to hold a liquid sample.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242
has super-classes
NMR probe c

list-mode data filec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000021

A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.
Source
group:Flow Cytometry community
Example
An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used.
has super-classes
information content entity c

liverc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002107

An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
has super-classes
material anatomical entity c

living in endemic areac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110018

a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely
Source
IEDB
has super-classes
environmental proximity to infectious agent c

living with infected household contactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110017

a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent
Source
IEDB
has super-classes
environmental proximity to infectious agent c

loess fittingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200116

A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda).
Source
ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101.
has super-classes
curve fitting data transformation c
achieves_planned_objective op some curve fitting objective c

loess global transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200023

A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation.
Source
OTHER: Editor's generalization based on MGED Ontology term
has super-classes
loess transformation c
has sub-classes
loess global transformation one-channel c, loess global transformation two-channel c

loess global transformation one-channelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200013

A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
Source
OTHER: Editor's generalization based on MGED Ontology term
Example
Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
has super-classes
loess global transformation c

loess global transformation two-channelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200015

A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
Source
OTHER: Editor's generalization based on MGED Ontology term
Example
Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
has super-classes
loess global transformation c

loess group transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200024

A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs.
Source
OTHER: Editor's generalization based on MGED Ontology term
has super-classes
loess transformation c
has sub-classes
loess group transformation one-channel c, loess group transformation two-channel c

loess group transformation one-channelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200018

A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
Source
OTHER: Editor's generalization based on MGED Ontology term
Example
A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
has super-classes
loess group transformation c

loess group transformation two-channelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200019

A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
Source
OTHER: Editor's generalization based on MGED Ontology term
Example
A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
has super-classes
loess group transformation c

loess scale group transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200025

A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling.
Source
OTHER: Editor's generalization based on MGED Ontology term
has super-classes
scaling data transformation c
achieves_planned_objective op some scaling objective c
immediately preceded by op some loess group transformation c
has sub-classes
loess scale group transformation one-channel c, loess scale group transformation two-channel c

loess scale group transformation one-channelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200010

A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar.
Source
OTHER: Editor's adjustment based on MGED Ontology term
Example
Loess scale group normalization applied to data from two one-channel expression microarray assays.
has super-classes
loess scale group transformation c

loess scale group transformation two-channelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200012

A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar.
Source
OTHER: Adjusted from MGED Ontology
Example
Loess scale group normalization applied to data from a two-channel expression microarray assay.
has super-classes
loess scale group transformation c

loess transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200071

A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves.
Source
OTHER: Editor's generalization based on MGED Ontology term
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c
has sub-classes
loess global transformation c, loess group transformation c

log basec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200141

The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1.
Source
WEB: http://en.wikipedia.org/wiki/Logarithm
has super-classes
mathematical feature c
has_feature_value dp some float

log-log curve fittingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200004

A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points.
Source
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446
Example
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution.
has super-classes
curve fitting data transformation c
achieves_planned_objective op some curve fitting objective c

logarithmic transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200094

A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
Source
WEB: http://en.wikipedia.org/wiki/Logarithm
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

logarithmic voltage amplifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400066

A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH
has super-classes
voltage amplifier c

logical transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200011

A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation.
Source
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Example
This type of transformation is typically used in flow cytometry.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

logistic-log curve fittingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200002

A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n).
Source
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
Example
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve.
has super-classes
curve fitting data transformation c
achieves_planned_objective op some curve fitting objective c

logit-log curve fittingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200003

A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points.
Source
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
Example
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively.
has super-classes
curve fitting data transformation c
achieves_planned_objective op some curve fitting objective c

long pass filterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400067

A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm.
Source
http://en.wikipedia.org/wiki/high-pass_filter
Example
750 LP filter
has super-classes
optical filter c

longitude coordinate measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001621

A measurement datum that is the measure of the longitude coordinate of a site.
Source
NIAID GSCID-BRC metadata working group
has super-classes
measurement datum c

longitudinal data analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200082

Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time.
has super-classes
data transformation c
achieves_planned_objective op some correlation study objective c

longitudinal mass measurement assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600026

A process in which the mass of a material is measured at two or more time points
Source
OBI branch derived
Example
The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection
has super-classes
assay c
has_specified_input op some organism c
has_specified_output op some measurement datum c
achieves_planned_objective op some assay objective c

looking up a centrally registered identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000580

A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
Example
Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
has super-classes
planned process c
has_specified_input op some centrally registered identifier symbol c
has_specified_output op some information content entity c
has participant op some centrally registered identifier registry c

loop designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500009

A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
Source
MO_912
Example
PMID: 12933549
has super-classes
study design c

lot numberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000132

A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
has super-classes
symbol c

lowess global transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001481

A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.
Source
MO_692 lowess_global_normalization
has super-classes
lowess transformation c

lowess group transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001474

A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
Source
MO_861 lowess_group_normalization
has super-classes
lowess transformation c

lowess transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001477

A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.
Source
MO_720 lowess_normalization
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c
has sub-classes
lowess global transformation c, lowess group transformation c

LSR2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400068

A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use.
Source
http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf
Example
LSR2 at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

LSRFortessa X-20c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001871

A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously.
Source
http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg
has super-classes
flow cytometer analyzer c
is_manufactured_by op value Becton Dickinson (BD Biosciences)

luciferinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_25078

A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
has super-classes
molecular entity c

Luminex 100c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400069

The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette.
Source
http://www.luminexcorp.com/products/luminex_100IS.html
has super-classes
flow cytometer analyzer c

Luminex 200c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400070

A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation
Source
http://www.luminexcorp.com/support/faqs.html
has super-classes
flow cytometer analyzer c

lungc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002048

Respiration organ that develops as an oupocketing of the esophagus.
has super-classes
material anatomical entity c

lung specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002534

A specimen that is derived from lung.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some lung c))
has super-classes
specimen from organism c

lymph nodec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000029

Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
has super-classes
material anatomical entity c

lymph node cell specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110041

A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
Source
IEDB
has super-classes
processed specimen c
cell specimen c
is_specified_output_of op some organ harvesting c and (has_specified_input op some lymph node c)

lymphocytec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000542

A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
has super-classes
mononuclear cell c
has sub-classes
B cell c, T cell c

lymphotoxin A productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032641

The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
tumor necrosis factor superfamily cytokine production c
has sub-classes
epitope specific lymphotoxin A production by T cells c

lyophilization storagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000927

a storage process with input material entity and output freeze dried material for long time storage
can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
Source
Example
has super-classes
storage c
has_specified_input op some material entity c
achieves_planned_objective op some material maintenance objective c

lyophilized specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000965

a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
Source
MO_589 freeze_dried_sample
Example
freezing dried DNA
is equivalent to
(is_specified_output_of op some lyophilization storage c and (has_specified_input op some has role op some specimen role c)) and (has role op some specimen role c)
has super-classes
specimen with known storage state c
is disjoint with
frozen specimen c, paraffin specimen c, fresh specimen c, agar stab specimen c

lyophilizerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001087

A device that is used to freeze dry material.
Source
http://en.wikipedia.org/wiki/Freeze_drying
has super-classes
device c
has function op some freeze function c
has function op some mechanical function c

MA transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200150

An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation.
Source
PERSON: Elisabetta Manduchi
Example
MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2.
has super-classes
data transformation c

macromoleculec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33839

A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
has super-classes
molecular entity c
has sub-classes
denatured polymer c, methylated polymer c, nucleic acid c, peptide c

macromolecule localizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0033036

Any process in which a macromolecule is transported to, or maintained in, a specific location.
has super-classes
biological_process c

macrophagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000235

A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
has super-classes
cell c

macrophage inflammatory protein-1 alpha productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071608

The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific macrophage inflammatory protein-1 alpha production by T cells c

macrophage inflammatory protein-1 gamma productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071607

The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific macrophage inflammatory protein-1 gamma production by T cells c

macrophage migration inhibitory factor productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0044807

The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

MACS Quantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400071

A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications.
Source
http://www.miltenyi.com
has super-classes
flow cytometer analyzer c

magic angle spinning rotorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000523

A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle.
Source
WEB:<http://www.freepatentsonline.com/4352066.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130
has super-classes
device c
part of op some NMR instrument c

magnify functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000369

A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
has super-classes
function c

maintaining cell culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600024

a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
Source
OBI branch derived
Example
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
has super-classes
material maintenance c
has_specified_input op some cultured cell population c
has_specified_input op some culture medium c or cell freezing medium c
has_specified_output op some cultured cell population c
achieves_planned_objective op some material maintenance objective c

major histocompatibility typing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002122

A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined.
Source
http://www.ncbi.nlm.nih.gov/pubmed/27516207, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628004/
Example
Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire.
has super-classes
genotyping assay c

malec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000384

A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
has super-classes
biological sex c

Mammaliac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_40674

has super-classes
Amniota c
has sub-classes
Euarchontoglires c

manual injection systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000476

The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064
has super-classes
sample injection system c

manufacturerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000835

A person or organization that has a manufacturer role
is equivalent to
(Homo sapiens c or organization c) and (has role op some manufacturer role c)
has super-classes
material entity c

manufacturer rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000571

Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
Source
OBI
Example
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
has super-classes
role c
inheres in op some Homo sapiens c or organization c
realized in op only manufacturing c
has sub-classes
array manufacturer role c

manufacturingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000457

Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Source
GROUP: OBI PlanAndPlannedProcess Branch
is equivalent to
achieves_planned_objective op some manufacturing objective c
has super-classes
material processing c
has_specified_input op some material entity c
has_specified_output op some processed material c

manufacturing objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000458

is the objective to manufacture a material of a certain function (device)
Source
GROUP: OBI PlanAndPlannedProcess Branch
has super-classes
material transformation objective c

massc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000125

A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
has super-classes
quality c

mass analyzerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000345

A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
Source
http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer
Example
The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
has super-classes
measurement device c
material separation device c
has function op some material separation function c
has function op some measure function c

mass measurement assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000445

a process to determine the mass of an evaluant
Philippe Rocca-Serra
Source
OBI
Example
The patients was weighed and mass was determined to be 47 kilograms
has super-classes
assay c
realizes op some evaluant role c and (role of op some material entity c)
has_specified_input op some material entity c and (has role op some evaluant role c)
has_specified_output op some mass measurement datum c
achieves_planned_objective op some assay objective c

mass measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000414

A scalar measurement datum that is the result of measurement of mass quality
has super-classes
scalar measurement datum c
(has measurement unit label op only mass unit c) and (is quality measurement of op only mass c)

mass selective detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000569

A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier.
Source
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198
has super-classes
gas chromatography detector c

mass spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000049

A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
Source
http://en.wikipedia.org/wiki/Mass_spectrometry
Example
LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
has super-classes
measurement device c
(has part op some mass analyzer c) and (has part op some ion source c) and (has part op some ion detector c)
has_supplier op some Homo sapiens c or organization c
bearer of op some device setting c
has function op some measure function c
has sub-classes
tandem mass spectrometer c

mass spectrometry analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200085

A data transformation which has the objective of spectrum analysis.
is equivalent to
achieves_planned_objective op some spectrum analysis objective c
has super-classes
data transformation c
has sub-classes
centroid mass spectrum c, characteristic path length calculation c, continuum mass spectrum c, gas chromatography mass spectrometry c, tandem mass spectrometry c

mass spectrometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000470

An assay that identifies the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles.
Source
Philippe Rocca-Serra
Example
Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides.
is equivalent to
assay c and ((realizes op some function c and (inheres in op some mass spectrometer c)) and (has_specified_input op some mass spectrometer c))
has super-classes
assay c
has sub-classes
peptide mass fingerprinting c

mass spectrometry assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001654

A B cell epitope qualitative binding to antibody assay that uses a mass spectrometry assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some mass spectrometry assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

mass spectrometry assay measuring MHC ligand processing and presentationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001478

A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands
Source
IEDB
is equivalent to
assay measuring MHC ligand processing and presentation c and (has part op some mass spectrometry assay c)
has super-classes
assay measuring MHC ligand processing and presentation c
has sub-classes
mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC c, mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC c

mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHCc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001489

A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC.
Source
IEDB
has super-classes
mass spectrometry assay measuring MHC ligand processing and presentation c
has part op some mass spectrometry assay c

mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHCc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001510

A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC.
Source
IEDB
has super-classes
mass spectrometry assay measuring MHC ligand processing and presentation c
has part op some mass spectrometry assay c

mass unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000002

A unit which is a standard measure of the amount of matter/energy of a physical object.
has super-classes
measurement unit label c
has members
gram ni, kilogram ni, microgram ni, milligram ni, nanogram ni, picogram ni

mass value specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001929

A value specification that specifies the mass of some thing.
has super-classes
scalar value specification c
specifies value of op some mass c
has measurement unit label op only mass unit c

mast cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000097

A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
has super-classes
cell c

matched pairs designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500005

A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
Source
http://www.holah.karoo.net/experimentaldesigns.htm
Example
PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.
has super-classes
study design c

material acquisitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600010

An acquisition in which possession of a material entity is gained.
Source
IEDB
Example
Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI.
has super-classes
acquisition c
has_specified_output op some material entity c
is disjoint with
material processing c

material analysis servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001547

A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
Source
PERSON: Matthew Brush
Example
Services performing DNA sequencing or Cell Analysis
is equivalent to
material service c and (provides_service_consumer_with op some assay c)
has super-classes
material service c
has sub-classes
sequencing service c

material anatomical entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000465

Anatomical entity that has mass.
has super-classes
material entity c
has sub-classes
adrenal gland c, aorta c, brain c, breast c, colon c, coronary artery c, cortex of kidney c, dermis c, esophagus mucosa c, heart c, hypodermis c, left cerebral hemisphere c, liver c, lung c, lymph node c, mouth c, mucosa of nasopharynx c, mucosa of oropharynx c, multi-tissue structure c, organism substance c, pancreas c, pituitary gland c, placenta c, prostate gland c, right cerebral hemisphere c, skin of body c, spleen c, stomach c, strand of hair c, thyroid gland c, tibial artery c, tissue c, urinary bladder c, vein c

material combinationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000652

is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
Source
bp
Example
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is equivalent to
achieves_planned_objective op some material combination objective c
has super-classes
material processing c
has_specified_input op some material entity c
has_specified_output op some material entity c
has sub-classes
adding a material entity into a target c, creating a mixture of molecules in solution c, pooling specimens c

material combination functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000928

A material separation function is a function that decreases the resolution between two or more material entities.
Source
OBI
Example
A stirrer has a material combination function
has super-classes
function c

material combination objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000686

is an objective to obtain an output material that contains several input materials.
Source
bp
has super-classes
material transformation objective c
has sub-classes
adding material objective c

material component separationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600014

a material processing in which components of an input material become segregated in space
Source
IEDB
Example
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
is equivalent to
achieves_planned_objective op some material separation objective c
has super-classes
material processing c
has_specified_input op some material entity c
has_specified_output op some material entity c
has sub-classes
DNA Subtraction c, blood harvesting c, cell collecting c, cell culture splitting c, centrifugation c, concentrate c, dialysis c, electrophoresis c, excision c, extraction c, filtration c, gradient separation c, immunoprecipitation c, isolation of cell culture supernatant c, isolation of cell population c, lavage c, material portioning c, organ harvesting c, precipitation c, preparative chromatography c, purification c

material entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000040

An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
has super-classes
independent continuant c
has sub-classes
allergen c, anatomical cluster c, antigen c, atom c, capsule shell c, cell c, cellular_component c, chemical solution c, collection of specimens c, environmental material c, enzyme c, epitope c, fiat object c, glucose in solution c, growth environment c, guar gum c, immunogen c, infection c, manufacturer c, material anatomical entity c, material information bearer c, material to be added c, molecular entity c, object c, object aggregate c, organism c, organization c, population c, processed material c, protein complex c, scattered molecular aggregate c, sequence annotation provider c, soil c, specimen c, target of material addition c, vaccine c
is in domain of
bound_to op, has 2D boundary op, has disposition to bind op, has_supplier op, is_manufactured_by op
is in range of
bound_to op, has disposition to bind op
is disjoint with
immaterial entity c

material information bearerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000178

A material entity in which a concretization of an information content entity inheres.
Example
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
is equivalent to
material entity c and (bearer of op some concretizes op some information content entity c)
has super-classes
material entity c
has sub-classes
photographic print c, random access memory c

material maintenancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000838

a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
is equivalent to
achieves_planned_objective op some material maintenance objective c
has super-classes
planned process c
has sub-classes
maintaining cell culture c, storage c

material maintenance objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000806

An objective specification maintains some or all of the qualities of a material over time.
Source
PERSON: Bjoern Peters
has super-classes
objective specification c

material maintenance servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001515

A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.
Source
PERSON: Matthew Brush
Example
model organism colony maintanance
is equivalent to
material service c and (provides_service_consumer_with op some material maintenance c)
has super-classes
material service c
has sub-classes
material storage service c

material portioningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600018

a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
Source
OBI branch derived
Example
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
has super-classes
material component separation c
achieves_planned_objective op some portioning objective c

material processingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000094

A planned process which results in physical changes in a specified input material
Source
OBI branch derived
Example
A cell lysis, production of a cloning vector, creating a buffer.
is equivalent to
achieves_planned_objective op some material transformation objective c
has super-classes
planned process c
has_specified_input op some material entity c
has_specified_output op some processed material c
has_specified_input op only material entity c
has_specified_output op only material entity c
has sub-classes
Immunization in vitro c, addition of molecular label c, artificially induced DNA repair c, artificially induced cell membrane lysis c, artificially induced methylation c, artificially induced nucleic acid hybridization c, artificially induced reverse transcription c, cell co-culturing c, cell culture expansion c, cell cycle synchronization c, cell fixation c, cell permeabilization c, chemical cleavage c, cross linking c, denaturing c, dissection c, elution c, enzymatic amplification c, enzymatic cleavage c, enzymatic ligation c, establishing cell culture c, experimental disease induction c, genetic transformation c, histological sample preparation c, immobilization c, induced hemagglutination c, ionize process c, irradiation c, killing c, library preparation c, manufacturing c, material combination c, material component separation c, nucleic acid hybridization c, phage display library panning c, polymerization c, recombinant vector cloning c, sample preparation for assay c, selection by survival c, sequencing library multiplexing c, specimen family creation c, staining c, synthesis c, transplantation c, vaccine preparation c, washing c
is disjoint with
material acquisition c

material processing servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001563

A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer.
Source
PERSON: Carlo Torniai
Example
A service for cell line creation. A service providing cel line immortalization.
has super-classes
material service c
provides_service_consumer_with op some material processing c

material samplec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000747

A material entity that has the material sample role
Example
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
is equivalent to
material entity c and (has role op some material sample role c)
has super-classes
specimen c
has sub-classes
sample from organism c

material sample rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000740

A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
Example
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has super-classes
specimen role c

material sampling processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000744

A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
is equivalent to
specimen collection process c and (has_specified_input op some material entity c) and (has_specified_output op some material sample c)
has super-classes
specimen collection process c

material separation devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000932

A device with a separation function realized in a planed process
Example
flow cytometer
is equivalent to
has function op some material separation function c
has super-classes
device c
has sub-classes
centrifuge c, chromatography column c, chromatography device c, chromatography instrument c, denaturing high-performance liquid chromatography instrument c, droplet sorter c, electrophoresis system c, filter paper c, flow cytometer sorter c, liquid chromatography mass spectrometry platform c, mass analyzer c, microtome c, nucleic acid extraction/purification instrument c, obscuration bar c, optical filter c, protein separation apparatus c, rapid resolution column c, vibrotome c

material separation functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000372

A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
has super-classes
function c
has sub-classes
filter function c, sort function c

material separation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000639

is an objective to transform a material entity into spatially separated components.
Source
PPPB branch
Example
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is equivalent to
portioning objective c or separation into different composition objective c
has super-classes
material transformation objective c
has sub-classes
portioning objective c, separation into different composition objective c

material servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001528

A service which has a material entity as specified input and/or specified output.
Source
PERSON: Carlo Torniai
Example
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
is equivalent to
service c and (provides_service_consumer_with op some (has_specified_input op some material entity c) or (has_specified_output op some material entity c))
has super-classes
service c
has sub-classes
material analysis service c, material maintenance service c, material processing service c, material transport service c

material storage servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001557

A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
Source
PERSON: Matthew Brush
Example
A service that offers liquid nitrogen stroage.
is equivalent to
material service c and (provides_service_consumer_with op some storage c)
has super-classes
material maintenance service c

material supplier rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000018

a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Example
Jackson Labs is an organization which provide mice as experimental material
has super-classes
service provider role c

material to be addedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110108

a material that is added to another one in a material combination process
Source
IEDB
Example
A mixture of peptides that is being added into a cell culture.
is equivalent to
has role op some material to be added role c
has super-classes
material entity c
has sub-classes
cloning vector c

material to be added rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000319

material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
Source
OBI
Example
drug added to a buffer contained in a tube; substance injected into an animal;
has super-classes
role c
has sub-classes
cloning vector role c

material transformation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000456

an objective specifiction that creates an specific output object from input materials.
Source
GROUP: OBI PlanAndPlannedProcess Branch
Example
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has super-classes
objective specification c
has sub-classes
device creation objective c, genetic transformation objective c, manufacturing objective c, material combination objective c, material separation objective c

material transport servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001580

A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer.
Source
PERSON: Carlo Torniai
Example
A service for chemical disposal
has super-classes
material service c

mathematical featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200140

feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation
Source
PERSON: James Malone
has super-classes
data transformation c
has sub-classes
exponential base c, log base c, number of variables c, polynomial degree c
is in domain of
has_feature_value dp

mature NK T cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000814

A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
has super-classes
alpha-beta T cell c

mean centeringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200029

A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input.
Source
PERSON: Elisabetta Manduchi
Example
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

mean-centered datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302868

a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value
is equivalent to
is_specified_output_of op some mean centering c
has super-classes
normalized data set c

measure functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000453

Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
Example
A glucometer measures blood glucose concentration, the glucometer has a measure function.
has super-classes
function c
function of op some processed material c
realized in op only has_specified_output op some measurement datum c
has sub-classes
image acquisition function c

measured expression levelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000101

A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
Source
OBI Data Transformation branch
Example
Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
has super-classes
measurement datum c

measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000109

A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
Source
OBI_0000305
group:OBI
Example
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has super-classes
data item c
has value specification op some value specification c
has sub-classes
3D structural organization datum c, categorical measurement datum c, dose c, fluorescent reporter intensity c, latitude coordinate measurement datum c, longitude coordinate measurement datum c, measured expression level c, number of lost events computer c, number of lost events electronic c, number of particles in subset c, parameter threshold c, ratio of collected to emitted light c, scalar measurement datum c, sequence data c, spike train datum c, survival rate c, time stamped measurement datum c
is in domain of
is quality measurement of op

measurement devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000832

A device in which a measure function inheres.
Source
OBI
Example
A ruler, a microarray scanner, a Geiger counter.
is equivalent to
device c and (has function op some measure function c)
has super-classes
device c
has sub-classes
DNA sequencer c, NMR instrument c, NMR probe c, Sysmex CA-6000 Coagulation Analyzer c, angiograph c, balance c, calorimeter c, centrifuge c, chromatography device c, coagulation analyzer c, column chromatography detector c, cytometer c, densitometer c, differential pressure gauge c, diffractometer c, electrical conductivity detector c, evaporative light scattering detector c, fluid pressure regulator c, fluorescene detector c, gamma counter c, glucometer c, image creation device c, ion detector c, liquid chromatography mass spectrometry platform c, mass analyzer c, mass spectrometer c, micro electrode c, microhardness tester c, micropipette c, microplate reader c, multichannel pipette c, multiple wavelength detector c, nucleic acid sequencer c, oscilloscope c, pH meter c, patch clamp device c, photodetector c, photomultiplier tube c, protein sequencer c, pulsed amperometric detector c, radiation measurement device c, refractive index detector c, scintillation counter c, spectrophotometer c, surface plasmon resonance instrument c, variable wavelength detector c, voltage clamp device c

measurement unit labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000003

A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
Example
Examples of measurement unit labels are liters, inches, weight per volume.
has super-classes
datum label c
has sub-classes
concentration unit c, frequency unit c, length unit c, mass unit c, pressure unit c, rate unit c, substance unit c, temperature unit c, time unit c, volume unit c, volumetric flow rate unit c
is in range of
has measurement unit label op

measuring glucose concentration in blood serumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000418

An assay that determines the concentration of glucose molecules in a blood serum sample
has super-classes
analyte assay c
realizes op some evaluant role c and (role of op some blood serum specimen c)
realizes op some analyte role c and (role of op some glucose c)

measuring neural activity in the caudate nucleusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000812

The process of measuring neural activity in the caudate nucleus
Source
Jessica Turner, NIF, Dirk Derom, OBI
Example
An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus
has super-classes
extracellular electrophysiology recording c
realizes op some measure function c and (inheres in op some micro electrode c)
occurs in op some caudate nucleus c

mechanical balancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001091

A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight).
Source
http://www.britannica.com/EBchecked/topic/49765/balance
has super-classes
balance c

mechanical functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000379

A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
Source
http://en.wikipedia.org/wiki/Mechanical_work
has super-classes
function c

median calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200119

A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
Source
PERSON: James Malone
PERSON: Monnie McGee
has super-classes
center calculation data transformation c
descriptive statistical calculation data transformation c
(has_specified_output op some center value c) and (achieves_planned_objective op some center calculation objective c)
achieves_planned_objective op some descriptive statistical calculation objective c

median centeringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200030

A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input.
Source
PERSON: Elisabetta Manduchi
Example
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

MeDIP-seq assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000693

is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
Source
adapted from wikipedia
Example
PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
has super-classes
DNA methylation profiling assay c
assay using chromatin immunoprecipitation c
sequencing assay c
has part op some immunoprecipitation c
has part op some library preparation c
has part op some Helicos sequencing c or SOLiD sequencing c or Solexa sequencing c or pyrosequencing c
has_specified_input op some deoxyribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some sequence data c and (is about op some regulation of DNA methylation c)
has_specified_output op some sequence data c and (is about op some primary structure of DNA macromolecule c and (is about op some regulation of DNA methylation c) and (is about op some deoxyribonucleic acid c and (has quality op some DNA residue methylation c)))
achieves_planned_objective op some assay objective c

membrane-bounded organellec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0043227

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
has super-classes
cellular_component c
has sub-classes
mitochondrion c

merging objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200189

A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets.
Source
PERSON: Data Transformation Branch
Example
merging of columns from two different data sets
has super-classes
data transformation objective c

metabolite profilingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000366

metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
Source
OBI
Example
Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
has super-classes
assay c
has_specified_input op some specimen c
has_specified_output op some measurement datum c
achieves_planned_objective op some assay objective c

metal vapor laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400073

A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
Gold vapor laser, Helium-cadmium metal-vapor laser
has super-classes
gas laser c
has sub-classes
helium cadmium ion laser c

methodology testing objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000208

Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
has super-classes
objective specification c
has sub-classes
hardware testing objective c, protocol testing objective c, software testing objective c

methods sectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000317

A part of a publication about an investigation that is about the study design of the investigation
Example
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
has super-classes
document part c
is about op some study design c

methylated polymerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302847

A methylated polymer which has artificially acquired one or more methyl groups
Source
OBI Biomaterial
Example
Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922
is equivalent to
macromolecule c and (is_specified_output_of op some artificially induced methylation c)
has super-classes
macromolecule c
processed material c

Methylation 27K BeadChipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002005

A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution.
Source
http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf
Example
Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139
has super-classes
Illumina methylation BeadChip c

Methylation 450K BeadChipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002004

A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution.
Source
http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn
Example
Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710
has super-classes
Illumina methylation BeadChip c

methylation-sensitive restriction enzyme sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001861

An assay that identifies unmethylated CpGs by use of methylation sensitive restriction enzymes to fragment DNA.
Source
Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842]
Example
Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842]
has super-classes
DNA sequencing c
DNA methylation profiling by high throughput sequencing assay c
has part op some DNA sequencing c
has part op some library preparation c
has part op some specific enzymatic cleavage c
has_specified_input op some deoxyribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c and (is about op some regulation of DNA methylation c)
achieves_planned_objective op some epigenetic modification identification objective c
has participant op some DNA sequencer c

methylation-specific polymerase chain reaction c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001684

is an assay which uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
Source
PMID:8790415
Example
Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID: 18219662
has super-classes
assay c

MethylC-Capture sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002094

A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing.
Source
Allum et al., Nature Commun. 2015 (PMID: 26021296)
Example
MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants.
has super-classes
bisulfite sequencing c

mhc binding predictionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200059

An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule.
Source
PERSON: Helen Parkinson
has super-classes
sequence analysis data transformation c
achieves_planned_objective op some sequence analysis objective c

MHC ligand assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002075

An immune epitope assay that detects either the processing and presentation of a ligand by an antigen presenting cell or the binding of a ligand to an MHC molecule.
Source
IEDB
is equivalent to
immune epitope assay c and (has_specified_output op some information content entity c and (is about op some MHC protein complex binding to ligand c))
has super-classes
binding assay c
immune epitope assay c
has sub-classes
assay measuring MHC ligand processing and presentation c, assay measuring binding of a MHC:ligand complex c

MHC protein complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0042611

A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
has super-classes
protein complex c

MHC protein complex binding to ligandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001503

The process in which a ligand binds to an MHC molecule to form a stable complex
Source
IEDB
Example
The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex.
has super-classes
binding c
binding c and (realizes op some disposition c and (inheres in op some material entity c and (bound_to op some MHC protein complex c)))

MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110179

A T cell epitope qualitative binding assay that uses an MHC multimer staining assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex c and ((realizes op some reagent role c and (inheres in op some fluorescently labeled MHC multimer c)) and (has_specified_input op some fluorescently labeled MHC multimer c)) and (has part op some flow cytometry assay c)
has super-classes
flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex c

MHC:epitope complex binding to TCRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110057

a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule.
Source
IEDB
has super-classes
binding c
epitope binding by adaptive immune receptor c
realizes op some disposition to be bound by an adaptive immune receptor c and (inheres in op some material entity c and (bound_to op some T cell receptor complex c) and (bound_to op some MHC protein complex c))
realizes op some restricting MHC role c and (inheres in op some MHC protein complex c)

micro electrodec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000816

An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
Source
Jessica Turner, Dirk Derom
Example
A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
has super-classes
measurement device c
is_manufactured_by op some organization c
has function op some measure function c

microarrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400147

A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
Source
PERSON: Chris Stoeckert
Example
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
has super-classes
assay array c
has sub-classes
DNA microarray c, protein microarray c

microarray assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001985

An analyte assay where binding of the analyte to immobilized matrix is measured.
Source
IEDB
Example
Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray.
is equivalent to
analyte assay c and ((realizes op some function c and (inheres in op some microarray c)) and (has_specified_input op some microarray c))
has super-classes
analyte assay c

microarray assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002053

A B cell epitope qualitative binding to antibody assay that uses a microarray.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some microarray c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

microarray platformc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000052

A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
Source
OBI Instrument branch
has super-classes
physical store c
has part op some microarray c
has function op some environment control function c

microarray wash stationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400119

a device that is used to wash Affymetrix-type arrays.
Source
MO_626 wash_station
Example
ArrayIt(r) Microarray Wash Station
has super-classes
physical store c
has function op some environment control function c

microcentrifugec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001100

A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint.
Source
http://en.wikipedia.org/wiki/Laboratory_centrifuge
has super-classes
centrifuge c

micrococcal nuclease digestion followed by high throughput sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001924

An assay to identify nucleosome positioning by genome wide sequencing of regions senstative to digestion by micrococal nuclease
Source
Johnson et al. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006 Dec;16(12):1505-16. [PMID:17038564]
Example
Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607]
has super-classes
sequencing assay c
has part op some library preparation c
has part op some non specific enzymatic cleavage c
realizes op some evaluant role c and (role of op some deoxyribonucleic acid c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some protein and DNA interaction identification objective c
has participant op some DNA sequencer c

micrococcal nuclease digestion followed by tiling array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002037

An array based nucleic acid structure mapping assay to identify nucleosome positions, genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling arrays.
Example
pmid:17873876
has super-classes
array based nucleic acid structure mapping assay c

microdissection instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001123

A device that is used for the dissection of tissues under magnification.
Source
http://medical-dictionary.thefreedictionary.com/microdissection
has super-classes
device c
has function op some mechanical function c

microhardness testerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001089

A hardness testing device that is used in light-optical microscopes.
Source
United States Patent 4611487
has super-classes
measurement device c
has function op some measure function c

micromanipulatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000935

A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand.
Source
http://en.wikipedia.org/wiki/Micromanipulator
has super-classes
device c
has function op some mechanical function c

micropipettec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001128

A microinjection device that is used to measure very small volumes of liquids.
Source
http://www.answers.com/topic/micropipette
has super-classes
measurement device c
has function op some mechanical function c
has function op some measure function c
has sub-classes
electronic repeater pipette c

micropipette pullerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001124

A device that is used to fabricate glass micropipettes.
Source
http://en.wikipedia.org/wiki/Micropipette
has super-classes
device c
has function op some mechanical function c

microplate readerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001058

A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
Source
http://en.wikipedia.org/wiki/Plate_reader
has super-classes
measurement device c
has function op some measure function c
has sub-classes
ELISA microplate reader c, multimode microplate reader c

microplate washerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001113

A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
Source
http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037
has super-classes
device c
has function op some mechanical function c
has sub-classes
ELISA microplate washer c

microRNA profiling assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001926

A transcription profiling assay in which aims to quantify the microRNA species within a biological sample.
Source
Kolbert et al. Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues. PLoS One. 2013;8(1):e52517 [PMID: 23382819]
is equivalent to
transcription profiling assay c and (has_specified_output op some measured expression level c and (is about op some miRNA c))
has super-classes
transcription profiling assay c
realizes op some evaluant role c and (role of op some ribonucleic acid c)
has sub-classes
microRNA profiling by array assay c, microRNA profiling by high throughput sequencing assay c

microRNA profiling by array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001335

An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome.
Source
EFO_0000753 microRNA profiling by array
has super-classes
microRNA profiling assay c
realizes op some analyte role c and (role of op some ribonucleic acid c)
has_specified_input op some specimen c and (has part op some ribonucleic acid c)
has_specified_output op some measured expression level c and (is about op some miRNA c)
achieves_planned_objective op some transcription profiling identification objective c
has participant op some DNA microarray c

microRNA profiling by array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001323

A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome.
Source
Group: ArrayExpress production team
has super-classes
transcription profiling design c
has part op some transcription profiling identification objective c
is concretized as op some realized in op some (has part op some microRNA profiling by array assay c) and (has participant op some DNA microarray c)

microRNA profiling by high throughput sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001922

A RNA-seq assay in which high throughput sequencing technology is used to analyse the microRNA component of the transcriptome.
Source
http://www.ebi.ac.uk/efo/EFO_0002896
Example
Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). [PMID: 21731767]
has super-classes
RNA-seq assay c
microRNA profiling assay c
has part op some library preparation c
realizes op some evaluant role c and (role of op some ribonucleic acid c)
has_specified_output op some measured expression level c and (is about op some miRNA c)

microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400169

A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
Source
wikipedia
Example
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
has super-classes
image creation device c
has function op some magnify function c
has function op some image acquisition function c
has sub-classes
confocal microscope c, digital microscope c, electron microscope c, laser capture microdissection microscope c, optical microscope c, scanning force microscope c

microscope slidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400170

a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
Source
OBI biomaterial branch
Example
PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
has super-classes
device c
has function op some solid support function c

microscopy assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002119

An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
Source
http://www.ncbi.nlm.nih.gov/pubmed/21685355
Example
Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy.
is equivalent to
imaging assay c and ((realizes op some function c and (inheres in op some microscope c)) and (has_specified_input op some microscope c))
has super-classes
imaging assay c
has sub-classes
electron microscopy imaging assay c

microtiter platec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000192

A microtiter_plate is a flat plate with multiple wells used as small test tubes.
Source
http://en.wikipedia.org/wiki/Microtiter_plate
Example
A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
has super-classes
container c
has function op some contain function c

microtomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400168

A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
Source
PERSON: Daniel Schober
Example
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
has super-classes
material separation device c
has function op some material separation function c
has function op some mechanical function c

microtome knife makerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001073

A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some mechanical function c

microtome knife sharpenerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001093

A device that is used to sharpen knives used in microtomy.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some mechanical function c

microwave synthesis systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001061

A device that is used to apply microwave irradiation to chemical reactions.
Source
http://en.wikipedia.org/wiki/Microwave_chemistry
has super-classes
device c
has function op some excitation function c
has function op some synthesizing function c

milkc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001913

An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
has super-classes
organism substance c

milk specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002505

A specimen that is derived from milk.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some milk c))
has super-classes
specimen from organism c

minimal inhibitory concentrationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001514

A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound.
Source
Bjoern Peters, coordinated with Albert Goldfain
has super-classes
scalar measurement datum c
has measurement unit label op some concentration unit c
is about op some dose response curve c

miRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000276

Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
has super-classes
region c

MiSeqc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002003

A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.
Source
http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf
Example
Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301]
has super-classes
DNA sequencer c
is_manufactured_by op value Illumina

mitochondrionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0005739

A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
has super-classes
membrane-bounded organelle c

mixed argon-krypton gas laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400074

A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer.
Source
http://www.eio.com/repairfaq/sam/laserarg.htm
Example
argon-krypton laser in a cytometer
has super-classes
ion laser c

mixed lymphocyte reaction assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002120

A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators).
Source
http://www.ncbi.nlm.nih.gov/pubmed/14969764
Example
T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells.
has super-classes
cytometry assay c
(realizes op some reagent role c and (inheres in op some molecular label c)) and (has_specified_input op some molecular label c)

mixed sexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001338

A biological sex quality inhering in a population of multiple sexes.
has super-classes
quality c

mode calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200117

A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
Source
PERSON: James Malone
PERSON: Monnie McGee
has super-classes
center calculation data transformation c
descriptive statistical calculation data transformation c
(has_specified_output op some center value c) and (achieves_planned_objective op some center calculation objective c)
achieves_planned_objective op some descriptive statistical calculation objective c

model numberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000017

A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
has super-classes
symbol c

modular decompositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200040

Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins.
Source
editor
has super-classes
network analysis c

MoFloc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400075

A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium.
Source
http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16
Example
MoFlo at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

molecular crosslinkerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400121

a device that is able to chemically join two or more molecules.
Source
MO ?? cannot be found in MO
Example
Stratalinker
has super-classes
light emission device c
physical store c
has function op some light emission function c
has function op some environment control function c

molecular entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_23367

Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
has super-classes
material entity c
has sub-classes
(S)-1-(4-bromoacetamidobenzyl)EDTA c, 1,1-dihydroxy-3-ethoxy-2-butanone c, 5'-adenylyl sulfate c, 5-bromo-2'-deoxyuridine c, EDTA methidiumpropylamide c, N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide c, N-ethyl-N-nitrosourea c, N-methylisatoic anhydride c, acrylamide c, amino acid c, bromophenol blue c, chromium-51 c, cytochalasin c, deuterium atom c, diethyl pyrocarbonate c, dimethyl sulfate c, ethylenediaminetetraacetic acid c, fucoidan c, gadodiamide c, gadodiamide hydrate c, gadolinium atom c, gadolinium molecular entity c, gadoteridol c, glucose c, hydrogensulfite c, hydroxyl c, lead(0) c, luciferin c, macromolecule c, molecular label c, phenol red c, polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether c, proton c, rhodium atom c, ruthenium atom c, sodium chloride c, sodium citrate dihydrate c, sodium phosphate c, terbium atom c, tris c, tritiated thymidine c, water c

molecular feature identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000131

Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
has super-classes
biological feature identification objective c
has sub-classes
DNA replication identification objective c, chromosome conformation identification objective c, epigenetic modification identification objective c, transcription profiling identification objective c

molecular function identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001690

is an objective specification which aims to discover molecular function realized by a molecular entity
Source
OBI group
has super-classes
biological feature identification objective c

molecular labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/REO_0000280

a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
Source
OBI developer call, 3-12-12
is equivalent to
molecular entity c and (has role op some molecular label role c)
has super-classes
molecular entity c
has sub-classes
Alexa Fluor 532 c, Alexa Fluor 546 c, Alexa Fluor 555 c, Cy3 dye c, Cy5 dye c, biotin c, digoxigenin c, fluorescein c

molecular label rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/REO_0000171

a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
Source
OBI developer call, 3-12-12
has super-classes
role c
has sub-classes
dye role c, radiolabel role c

molecular-labeled materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001936

a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
Source
OBI developer call, 3-12-12
is equivalent to
material entity c and (has part op some molecular label c) and (is_specified_output_of op some addition of molecular label c)
has super-classes
processed material c
has sub-classes
fluorescently labeled MHC multimer c, labeled oligonucleotide c, labeled specimen c

molecular_functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0003674

Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
has super-classes
function c
has sub-classes
catalytic activity c

monocyte chemotactic protein-1 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071605

The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
chemokine production c
has sub-classes
epitope specific monocyte chemotactic protein-1 production by T cells c

mononuclear cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000842

A leukocyte with a single non-segmented nucleus in the mature form.
has super-classes
cell c
has sub-classes
lymphocyte c

monospecific T cell recognition assay measuring MHC ligand processing and presentationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001469

A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout.
Source
IEDB
has super-classes
assay measuring MHC ligand processing and presentation c
has part op some assay measuring binding of a T cell epitope:MHC:TCR complex c

mortal cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0009829

A cell line is able to support only a limited number of passages in vitro.
has super-classes
cell line c
has grain op some mortal cell line cell c
has grain op only mortal cell line cell c
is_specified_output_of op exactly 0 cell line immortalization c

mortal cell line cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000018

A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence.
has super-classes
cell line cell c

Mouse 385K Whole Genome CGH Tiling Arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002008

A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features.
Source
http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
Example
Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/
has super-classes
tiling microarray c
is_manufactured_by op value Nimblegen

Mouse 3x720K Whole Genome CGH Tiling Arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002009

A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features.
Source
http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
Example
Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584
has super-classes
tiling microarray c
is_manufactured_by op value Nimblegen

mouthc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000165

The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
has super-classes
material anatomical entity c

moving averagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200056

A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
Source
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
Example
The moving average is often used to handle data from tiling arrays.
has super-classes
averaging data transformation c
(has_specified_output op some average value c) and (achieves_planned_objective op some averaging objective c)

MPE-Fe(II) structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001008

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-MP as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:6209709
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some EDTA methidiumpropylamide c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

mucosa of nasopharynxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0005022

A mucosa that is part of a nasopharynx [Automatically generated definition].
has super-classes
material anatomical entity c

mucosa of oropharynxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0005023

A mucosa that is part of a oropharynx [Automatically generated definition].
has super-classes
material anatomical entity c

multi-tissue structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000481

Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
has super-classes
material anatomical entity c
has sub-classes
cerebellum c, peritoneum c, renal medulla c

multi-well platec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400076

A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader.
Source
http://www.nuncbrand.com/page.aspx?ID=301
Example
96 well plate, 48 multiwell plate
has super-classes
particle delivery vessel c

multichannel electronic pipettec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001083

A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations.
Source
http://www.faqs.org/patents/app/20090196797
has super-classes
multichannel pipette c

multichannel pipettec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001118

A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
Source
PERSON: Erik Segerdell
has super-classes
measurement device c
has function op some mechanical function c
has function op some measure function c
has sub-classes
multichannel electronic pipette c

multimode microplate readerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001090

A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
Source
PERSON: Erik Segerdell
has super-classes
microplate reader c

multiple linear regression analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200103

multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression.
Source
WEB:http://en.wikipedia.org/wiki/Linear_regression
has super-classes
regression analysis method c

multiple testing correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200089

A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
Source
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
is equivalent to
achieves_planned_objective op some multiple testing correction objective c
has super-classes
error correction data transformation c
has sub-classes
false discovery rate correction method c, family wise error rate correction method c, generalized family wise error rate correction method c, proportion of expected false positives correction method c, quantile number of false positives correction method c, quantile proportion of false positives correction method c, tail probability for the proportion of false positives correction method c

multiple testing correction objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000791

A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
Source
http://en.wikipedia.org/wiki/Multiple_Testing_Correction
Example
Application of the Bonferroni correction
has super-classes
error correction objective c

multiple wavelength detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000505

A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078
has super-classes
measurement device c
has function op some measure function c

multiplex ligation-mediated amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001914

A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation.
Source
web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/
has super-classes
polymerase chain reaction c
has part op some enzymatic ligation c

multiplexed sequencing libraryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001970

a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run.
Source
PRS for OBI
Example
http://www.ncbi.nlm.nih.gov/pubmed/24997861 Nat Methods. 2014 Aug;11(8):834-40. doi: 10.1038/nmeth.3022. Epub 2014 Jul 6. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
has super-classes
processed material c
has part op some multiplexing sequence identifier c
is_specified_output_of op some library preparation c and sequencing library multiplexing c

multiplexing sequence identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001967

A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library
Source
OBI
Example
We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. in http://www.ncbi.nlm.nih.gov/pubmed/22574170
has super-classes
deoxyribonucleic acid c
is_specified_input_of op some library preparation c and sequencing library multiplexing c

multispectral imaging flow cytometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400146

A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations.
Source
http://www.amnis.com/
has super-classes
image creation device c
has part op some flow cytometer c
has function op some information processor function c
has function op some image acquisition function c
has sub-classes
Amnis ImageStream c

Murinaec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_39107

has super-classes
Rodentia c
has sub-classes
Mus musculus c, Rattus norvegicus c

Mus musculusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10090

has super-classes
Murinae c

N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_59053

A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents.
has super-classes
molecular entity c

N-ethyl-N-nitrosoureac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_23995

A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups.
has super-classes
molecular entity c

N-methylisatoic anhydridec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_59054

A 3,1-benzoxazin-1,4-dione having an N-methyl substituent.
has super-classes
molecular entity c

n-to-1 designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500004

N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993).
Source
Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
has super-classes
cross over design c

N50c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001940

the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly
Source
adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html"
Example
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
has super-classes
scalar measurement datum c
has measurement unit label op some measurement unit label c
is about op some assembly c
is_specified_output_of op some sequence assembly process c
has sub-classes
contig N50 c, scaffold N50 c

nano pump systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000474

A pump system optimized for nano flow chromatography.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052
has super-classes
chromatography pump system c

nano-cap analysis of gene expression c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001673

nano-CAGE is a type of CAGE developed to work from very low amount (nanogram scale) of mRNA samples
Source
PMID: 20543846
Example
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. PMID:20543846
has super-classes
transcription profiling assay c
(assay c and (has_specified_input op some RNA extract c) and (has_specified_output op some data item c and (is about op some gene expression c))) and (achieves_planned_objective op some transcription profiling identification objective c)

narrative objectc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000006

A narrative object is an information content entity that is a set of propositions.
Source
OBI_0000013
group:OBI
Example
Examples of narrative objects are reports, journal articles, and patents submission.
has super-classes
information content entity c

nasal swab specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000917

A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination.
Source
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
Example
type of sample used in the PCIRN influenza network
has super-classes
specimen c
has role op some specimen role c

nasopharyngeal aspirate specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000914

A speciemn which derives from nasopharyngeal mucosa after aspiration.
Source
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
Example
type of sample used in the PCIRN influenza network
has super-classes
specimen c
has role op some specimen role c

native cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000003

A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
has super-classes
cell c

nCounter Human V2 miRNA Expression arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002013

An array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays.
Source
http://www.nanostring.com/media/pdf/PDS_nCounter_Human_v2_miRNA_Assay.pdf
Example
Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819
has super-classes
assay array c
is_manufactured_by op value NanoString Technologies

needlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000436

a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
Source
OBI Instrument
Example
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
has super-classes
device c
has function op some transfer function c

needle assemblyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000551

The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065
has super-classes
chromatography device c

negative binding datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001182

A binding datum that states that there is no significant disposition of two or more entities to form a complex
has super-classes
binding datum c

negative reference substance rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000214

a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response
Example
Saline solution
has super-classes
reference substance role c
realized in op only assay c
has sub-classes
placebo role c

neodymium-YAG laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400077

A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer.
Source
John Quinn
Example
Neodymium-YAG Laser in DURIP99 System
has super-classes
solid state laser c

network analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200080

A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network.
Source
PERSON: Richard Scheuermann
has super-classes
data transformation c
has sub-classes
edge quality calculation c, edge weighting c, modular decomposition c, network graph construction c, network graph quality calculation c, network subgraph quality calculation c, node quality calculation c

network graph constructionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200126

A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph.
Source
PERSON: Richard Scheuermann
has super-classes
network analysis c
has sub-classes
directed network graph construction c, weighted network graph construction c

network graph quality calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200147

A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole.
Source
PERSON: Richard Scheuermann
has super-classes
network analysis c
has sub-classes
global modularity calculation c

network subgraph quality calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200137

A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network.
Source
PERSON: Richard Scheuermann
has super-classes
network analysis c
has sub-classes
intra subgraph connectivity calculation c, quantitative subgraph degree calculation c, subgraph degree calculation c, subgraph in-degree calculation c, subgraph modularity calculation c, subgraph out-degree calculation c

Neurosporac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_5140

has super-classes
saccharomyceta c

NextSeq 500c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002021

A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
Source
http://systems.illumina.com/systems/nextseq-sequencer.html
has super-classes
DNA sequencer c
is_manufactured_by op value Illumina

nitrogen generatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000550

A gas generator that generates nitrogen gas.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034
has super-classes
gas generator c

nitrogen phosphorous detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000489

The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement.
Source
WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089
has super-classes
gas chromatography detector c

NMIA RNA structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001026

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses NMIA as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID: 15796531
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some N-methylisatoic anhydride c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

NMR assay determining the 3D structure of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001647

A B cell epitope 3D structure determination assay that uses a nuclear magnetic resonance assay.
Source
IEDB
is equivalent to
3D structure determining assay of a 3D B cell epitope:antibody complex c and (has part op some nuclear magnetic resonance 3D structure determination assay c) and (has_specified_output op some 3D structural organization datum c)
has super-classes
3D structure determining assay of a 3D B cell epitope:antibody complex c

NMR assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001662

A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some nuclear magnetic resonance 3D structure determination assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002054

A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c and (has part op some nuclear magnetic resonance 3D structure determination assay c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c

NMR consolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000499

A component of an NMR instrument that controls the activities of the other components.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015
has super-classes
device c
has sub-classes
tecmag NMR console c

NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000566

An Instrument which is used to carry out a NMR analysis of some sample.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059
has super-classes
measurement device c
has function op some measure function c
has sub-classes
Bruker NMR instrument c, JEOL NMR instrument c, Varian NMR instrument c, continuous wave NMR instrument c, fourier transformation NMR instrument c, tecmag NMR instrument c

NMR magnetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000517

A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.\n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185
has super-classes
device c
has sub-classes
Bruker NMR magnet c

NMR probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000516

Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.\n alt The instrument that transmits and receives radiofrequency to and from the NMR sample.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014
has super-classes
measurement device c
part of op some NMR instrument c
has function op some measure function c
has sub-classes
Bruker NMR probe c, JEOL NMR probe c, direct detection NMR probe c, flow probe c, imaging NMR probe c, indirect detection probe c, liquid NMR probe c, solid NMR probe c

NMR sample holderc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000484

An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212
has super-classes
device c
has sub-classes
Bruker MATCH tube holder system c

NMR sample tubec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000578

The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132
has super-classes
test tube c
part of op some NMR instrument c

NMR spectroscopyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000623

NMR spectroscopy is a process which exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures.
Source
adapted from Wikipedia
Example
Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202
has super-classes
assay c
achieves_planned_objective op some assay objective c

NMR tube washing systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000498

An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204
has super-classes
device c
has sub-classes
Bruker AutoClean system c

node degree calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200130

A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node.
Source
PERSON: Richard Scheuermann
has super-classes
node quality calculation c

node in-degree calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200132

A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node.
Source
PERSON: Richard Scheuermann
has super-classes
node quality calculation c

node out-degree calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200133

A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node.
Source
PERSON: Richard Scheuermann
has super-classes
node quality calculation c

node quality calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200129

A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network.
Source
PERSON: Richard Scheuermann
has super-classes
network analysis c
has sub-classes
node degree calculation c, node in-degree calculation c, node out-degree calculation c, node shortest path identification c, quantitative node degree calculation c

node shortest path identificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200134

A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network.
Source
PERSON: Richard Scheuermann
has super-classes
node quality calculation c

non specific enzymatic cleavagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600023

a protocol application to digest the fraction of input material that is susceptible to that enzyme
Source
OBI branch derived
Example
The use of agarase to digest an agar gel
has super-classes
enzymatic cleavage c

non-negative matrix factorizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200097

Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero.
Source
http://en.wikipedia.org/wiki/Non-negative_matrix_factorization
Example
Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix.
has super-classes
data transformation c

non-specific labelingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600019

The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial
Source
OBI branch derived
Example
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies.
has super-classes
addition of molecular label c

normal phase columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000482

A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097
has super-classes
chromatography column c

normalization data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200169

A normalization data transformation is a data transformation that has objective normalization.
Source
PERSON: James Malone
is equivalent to
(has_specified_output op some normalized data set c) or (achieves_planned_objective op some data normalization objective c)
has super-classes
data transformation c
has sub-classes
b transformation c, biexponential transformation c, box-cox transformation c, cosine transformation c, eh transformation c, exponential transformation c, hyperlog transformation c, linlog transformation c, loess transformation c, logarithmic transformation c, logical transformation c, lowess transformation c, mean centering c, median centering c, pareto scaling c, quantile transformation c, replicate analysis c, s transformation c, sine transformation c, soft independent modeling of class analogy analysis c, total intensity transformation paired c, total intensity transformation single c, unit-variance scaling c, variance stabilizing transformation c

normalization testing designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001214

A study design that tests different normalization procedures.
Source
MO_729 normalization_testing_design
has super-classes
study design c
has part op some software testing objective c
has part op some study design independent variable c and (is about op some normalization data transformation c)

normalized data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000451

A data set that is produced as the output of a normalization data transformation.
is equivalent to
is_specified_output_of op some normalization data transformation c
has super-classes
data set c
has sub-classes
mean-centered data c

northern blot analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000860

a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager
Example
PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K.
has super-classes
analyte assay c
realizes op some evaluant role c and (inheres in op some polyA RNA extract c)
realizes op some analyte role c and (inheres in op some scattered molecular aggregate c and (has grain op only nucleic acid c))
realizes op some complementary nucleotide probe role c and (inheres in op some nucleic acid c)
has_specified_output op some measurement datum c and (is about op some gene expression c)
achieves_planned_objective op some assay objective c

nothingc back to ToC or Class ToC

IRI: http://www.w3.org/2002/07/owl#Nothing

has super-classes
nothing c
has sub-classes
nothing c
is in domain of
obsolete property op
is in range of
obsolete property op

notified body rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000056

Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive
Source
OBI, CDISC
Example
The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
has super-classes
role of regulator of consumables and medical devices c

NTP-2000c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000735

a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents
has super-classes
processed material c
is_specified_output_of op some manufacturing c
has role op some feed role c

nuclear magnetic resonance 3D structure determination assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000182

A 3D structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample.
Source
IEDB
Example
Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013).
is equivalent to
3D structure determination assay c and ((realizes op some function c and (inheres in op some NMR instrument c)) and (has_specified_input op some NMR instrument c)) and (has_specified_output op some 3D structural organization datum c)
has super-classes
3D structure determination assay c

nuclear RNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000862

A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
Source
UPenn Group
Example
Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
has super-classes
RNA extract c
is_specified_output_of op some nuclear RNA extraction c

nuclear RNA extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000888

A RNA extraction process in which the desired output material is RNA in the nucleus.
Source
UPenn Group
has super-classes
RNA extraction c

nuclease S1c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000025471

A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof.
has super-classes
protein c

Nuclease S1 structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001035

a single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:363143
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c
realizes op some catalytic activity c and (inheres in op some nuclease S1 c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

nucleic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33696

A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
has super-classes
macromolecule c
has sub-classes
deoxyribonucleic acid c, genetic material c, nucleic acid restriction enzyme digest c, ribonucleic acid c

nucleic acid extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001010

An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
Source
UPenn Group
has super-classes
extract c
processed specimen c
(is_specified_output_of op some nucleic acid extraction c) and (has role op some specimen role c)
has grain op some nucleic acid c
has sub-classes
DNA extract c, RNA extract c

nucleic acid extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0666667

a material separation to recover the nucleic acid fraction of an input material
Source
OBI branch derived
Example
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
has super-classes
extraction c
has_specified_input op some sample from organism c or organism c or cultured cell population c
has_specified_output op some nucleic acid c
has sub-classes
DNA extraction c, RNA extraction c

nucleic acid extraction/purification instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001114

A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
Source
PERSON: Erik Segerdell
has super-classes
material separation device c
has function op some material separation function c
has sub-classes
DNA extraction/purification instrument c, RNA extraction/purification instrument c

nucleic acid hybridizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302903

a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
Source
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
Example
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
has super-classes
material processing c
realizes op some function c and (inheres in op some hybridization chamber c)

nucleic acid restriction enzyme digestc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000742

A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site
is equivalent to
nucleic acid c and (is_specified_output_of op some specific enzymatic cleavage c and (has_specified_input op some nucleic acid c) and (has participant op some restriction enzyme c))
has super-classes
nucleic acid c
processed material c

nucleic acid sequencerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001108

An device that is used to determine the order of nucleotides in nucleic acid sequences.
Source
PERSON: Erik Segerdell
has super-classes
measurement device c
has function op some measure function c

nucleic acid template rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000409

a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
Example
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
has super-classes
reference substance role c
inheres in op some nucleic acid c
realized in op only polymerase chain reaction c

nucleotide overhang cloningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000687

Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
Example
Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
has super-classes
recombinant vector cloning c

number of errorsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001873

a data item that is the number of times that a given process failed, as an integer
Source
PRS, AGB
Example
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. see table2
has super-classes
data item c
value specification c
is about op some process c
has specified value dp some integer

number of lost events computerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000269

A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role
Source
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
Example
0, 125, 787 events lost due to computer busy.
has super-classes
measurement datum c

number of lost events electronicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000125

A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.
Source
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
Example
74, 0, 14 events lost due to data acquisition electronic coincidence.
has super-classes
measurement datum c

number of particles in subsetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000119

A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
Source
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
Example
500, 200, 0
has super-classes
measurement datum c

number of variablesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200153

The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space.
Source
PERSON: Elisabetta Manduchi
has super-classes
mathematical feature c
has_feature_value dp some integer

numeralc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000029

A symbol that denotes a number.
has super-classes
symbol c
has sub-classes
integer numeral c

nutrient rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000204

a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.
Source
Wikipedia, feb 29, 2008
Example
Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
has super-classes
role c
inheres in op some material entity c
has sub-classes
complete nutrient role c

objectc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000030

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
has super-classes
material entity c

object aggregatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000027

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Source
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
Example
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
has super-classes
material entity c

objective specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000005

a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
Source
OBI Plan and Planned Process/Roles Branch
OBI_0000217
Example
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has super-classes
directive information entity c
has sub-classes
assay objective c, assay validation objective c, biological feature identification objective c, data transformation objective c, decision-theoretic analysis objective c, material maintenance objective c, material transformation objective c, methodology testing objective c, selective organism creation objective c, service provision objective c, specification of data to be generated in an investigation c, specimen collection objective c, training objective c
is in domain of
objective_achieved_by op
is in range of
achieves_planned_objective op

obscuration barc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400078

An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
Source
John Quinn
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
Example
obscuration bar in a flow cytometer
has super-classes
material separation device c
has function op some filter function c

observation designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0300311

observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
Source
OBI branch derived
Example
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
has super-classes
study design c

obsolescence reason specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000225

The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
is equivalent to
{ failed exploratory term , placeholder removed , terms merged , term imported , term split }
has super-classes
data about an ontology part c
has members
other ni, term imported ni, term split ni, terms merged ni

obsolete B cell epitope competitive binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001715

A competitive inhibition of binding assay using a assay
Source
IEDB (QTT)
has super-classes
Obsolete Class c

obsolete B cell epitope direct binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001712

A direct binding assay using a assay
Source
IEDB (QTT)
has super-classes
Obsolete Class c

obsolete B cell epitope specific X-ray crystallography assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001737

A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms
Source
IEDB (QTT)
has super-classes
Obsolete Class c

obsolete cell bound MHC binding constant determination assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001572

An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant.
Source
IEDB
has super-classes
Obsolete Class c

obsolete cell bound MHC direct binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001582

direct binding assay measuring MHC ligand binding using MHC derived from a cell
Source
IEDB (QTT)
has super-classes
Obsolete Class c

obsolete cell lysate MHC binding constant determination assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001560

An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant.
Source
IEDB
has super-classes
Obsolete Class c

obsolete cell lysate MHC competitive binding assay using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001574

competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
Source
IEDB (QTT)
has super-classes
Obsolete Class c

Obsolete Classc back to ToC or Class ToC

IRI: http://www.geneontology.org/formats/oboInOwl#ObsoleteClass

has super-classes
thing c
has sub-classes
biological vector role c, obsolete B cell epitope competitive binding assay c, obsolete B cell epitope direct binding assay c, obsolete B cell epitope specific X-ray crystallography assay c, obsolete MHC multimer staining assay c, obsolete T cell recognition of eluted MHC ligand assay c, obsolete cell bound MHC binding constant determination assay c, obsolete cell bound MHC direct binding assay c, obsolete cell lysate MHC binding constant determination assay c, obsolete cell lysate MHC competitive binding assay using radioactivity detection c, obsolete dependent continuant c, obsolete intracellular cytokine staining assay c, obsolete intracellular material detection by flow cytometry assay c, obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation c, obsolete purified MHC binding constant determination assay c, obsolete purified MHC direct binding assay c, obsolete2_binary digital entity c, obsolete2_binary executable c, obsolete2_digital document c, obsolete2_digital entity c, obsolete2_report figure c, obsolete2_text based digital entity c, obsolete_DNA ligase c, obsolete_DNA sequencing training service c, obsolete_activation c, obsolete_adipose tissue c, obsolete_ambidexterious handedness c, obsolete_anatomical entity c, obsolete_artifact c, obsolete_blinded medication role c, obsolete_cell line c, obsolete_cell line cell c, obsolete_collection (of entities of organismal origin) c, obsolete_defined processes c, obsolete_defined_material c, obsolete_defined_output c, obsolete_diethyl pyrocarbonate c, obsolete_digital quality c, obsolete_disease c, obsolete_documenting c, obsolete_dropout role c, obsolete_electrically powered device c, obsolete_enrollment c, obsolete_establishing a CRID registry c, obsolete_fragment derived from protein c, obsolete_general scalar measurement datum c, obsolete_handedness c, obsolete_heart c, obsolete_identification c, obsolete_identifier c, obsolete_immortal cell c, obsolete_immortal cell line culture c, obsolete_label role c, obsolete_left handedness c, obsolete_liver c, obsolete_material access provider role c, obsolete_material_entity c, obsolete_molecular concentration c, obsolete_occurrence of disease c, obsolete_peritoneum c, obsolete_platform c, obsolete_polymer c, obsolete_primary structure of protein c, obsolete_primary structure of sequence macromolecule c, obsolete_protocol service provider role c, obsolete_qualitative binding detection assay c, obsolete_report element c, obsolete_report table c, obsolete_right handedness c, obsolete_role of being first subject treated c, obsolete_sample population c, obsolete_specimen fixation function c, obsolete_study interpretation c, obsolete_study result c, obsolete_survival curve c, obsolete_training service provider role c, obsolete_trypsinized material c, obsolete_unit of measure c
is disjoint with
entity c

obsolete dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000005

A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
has super-classes
Obsolete Class c

obsolete intracellular cytokine staining assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000665

The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
Source
IEDB
Example
Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
has super-classes
Obsolete Class c

obsolete intracellular material detection by flow cytometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000856

An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
has super-classes
Obsolete Class c

obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001250

An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation
Source
IEDB (QTT)
has super-classes
Obsolete Class c

obsolete MHC multimer staining assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000667

An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer
Source
IEDB
Example
Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes.
has super-classes
Obsolete Class c

obsolete purified MHC binding constant determination assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001576

An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant.
Source
IEDB
has super-classes
Obsolete Class c

obsolete purified MHC direct binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001611

direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation
Source
IEDB (QTT)
has super-classes
Obsolete Class c

obsolete T cell recognition of eluted MHC ligand assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001540

An assay that identifies an MHC ligand using a T cell response assay as a readout
Source
IEDB
Example
Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell.
has super-classes
Obsolete Class c

obsolete2_binary digital entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000019

A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
Source
group:OBI
OBI_0000244
Example
MS Word document, ZIP file, DICOM file, JPEG file
has super-classes
Obsolete Class c

obsolete2_binary executablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000093

Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
Source
group:OBI
OBI_0000222
has super-classes
Obsolete Class c

obsolete2_digital documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000105

A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
Source
group:OBI
OBI_0000195
has super-classes
Obsolete Class c

obsolete2_digital entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000012

A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
Source
group:OBI
OBI_0000261
has super-classes
Obsolete Class c

obsolete2_report figurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000059

A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
Source
group:OBI
OBI_0000027
has super-classes
Obsolete Class c

obsolete2_text based digital entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000047

A text based digital entity is a digital entity that is encoded so that it only contains text characters.
Source
OBI_0000132
group:OBI
Example
XML file, C++ source code file
has super-classes
Obsolete Class c

obsolete_activationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302901

a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!)
Source
OBI-Branch
Example
PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63.
has super-classes
Obsolete Class c

obsolete_adipose tissuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302745

adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates.
Source
GROUP: OBI Biomaterial derived
Example
PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4.
has super-classes
Obsolete Class c

obsolete_ambidexterious handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000926

has super-classes
Obsolete Class c

obsolete_anatomical entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100015

An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
Source
MO
Example
Tissue, organ, system, sperm, blood or body location (arm).
has super-classes
Obsolete Class c

obsolete_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000008

has super-classes
Obsolete Class c

obsolete_blinded medication rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000223

Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance
Example
Inert pill shaped like aspirin tablet
115 patients received ipilimumab and blinded medication
has super-classes
Obsolete Class c

obsolete_cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100062

A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture).
1. The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, 'lines' are capable of being characterized and stably propagated over a period of time. A *new* cell line can be "established" not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quescent state for future use. 2. The definitional criteria provided here for the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.? 3. Definitinal criteria are intended to be sufficiently clear to specify what are and what are not instances of 'cell lines' in the real world. A 'HeLa cell line' would be a subset of all HeLa cells in the world - specifically any subset that has been derived through a shared continuous lineage wherein the cells have always been passaged together and thereby evolved together through the selective pressures imposed by this common history. Accordingly, 'HeLa cell line' would not be used to refer to the collection of all HeLa cells in a given lab, or all HeLa cells in the ATCC repository, as cells in these collections will likely not all share a common culture history. Rather, 'HeLa cell line' could refer to the collection of cells I am culturing at a given moment, or that I apply in an experiment (as such collections typically meet the criteria of having a shared propagation history). As noted above, it is such collections that are typically referred to in scientific discourse and publications. 4. Notably, the term 'line' has been alternately used by other terminologies and communities to refer to cultures that have been immortalized - ie has attained the capacity for indefinite propagation in vitro. In this ontology, we refer to such cell lines as 'immortal cell lines', and use the term 'cell line' to indicate any culture that has been passaged.
Source
OBI-CLO Alignment Working Group (Spring 2013)
Example
A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in "Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line". Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592.
He, Tong-Chuan, et al. \"Identification of c-MYC as a target of the APC pathway.\" Science 281.5382 (1998): 1509-1512. - \"To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene\". Note that common usage in the literature is often of the form \"a human colorectal cancer cell line\", as seen above. But such references to studies in \"a line\" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
has super-classes
Obsolete Class c

obsolete_cell line cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100055

A material entity that represents generations of a primary culture.
Source
GROUP: OBI Biomaterial Branch
has super-classes
Obsolete Class c

obsolete_collection (of entities of organismal origin)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302714

a collection is a bfo:aggregate object, that is a set of material object of the same kind
Source
PERSON: Philippe Rocca-Serra
Example
PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings]
has super-classes
Obsolete Class c

obsolete_defined processesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600065

Place holder class, see editor note
Source
OBI branch derived
has super-classes
Obsolete Class c

obsolete_defined_materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000233

Place holder class, Utility class to gather the defined classes
Source
OBI Biomaterial derived
has super-classes
Obsolete Class c

obsolete_defined_outputc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000449

This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process.
Example
example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation.
has super-classes
Obsolete Class c

obsolete_diethyl pyrocarbonatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000851

Replaced by CHEBI_59051 Diethylpyrocarbonate
has super-classes
Obsolete Class c

obsolete_digital qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000141

has super-classes
Obsolete Class c

obsolete_diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110055

placeholder to be imported from disease ontology
Source
IEDB
has super-classes
Obsolete Class c

obsolete_DNA ligasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000698

A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
has super-classes
Obsolete Class c

obsolete_DNA sequencing training servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000986

A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
has super-classes
Obsolete Class c

obsolete_documentingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000340

Source
wikipedia http://en.wikipedia.org/wiki/Documenting
Example
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has super-classes
Obsolete Class c

obsolete_dropout rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000205

Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role.
Source
OBI
Example
Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study)
has super-classes
Obsolete Class c

obsolete_electrically powered devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000972

a processed material created to have a function and which requires electrical power to execute
has super-classes
Obsolete Class c

obsolete_enrollmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000296

enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
Source
IEDB
Example
Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902
has super-classes
Obsolete Class c

obsolete_establishing a CRID registryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000576

a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
has super-classes
Obsolete Class c

obsolete_fragment derived from proteinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100039

A material entity which is derived from a protein
Source
GROUP: IEDB
Example
the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme
has super-classes
Obsolete Class c

obsolete_general scalar measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000987

has super-classes
Obsolete Class c

obsolete_handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000956

has super-classes
Obsolete Class c

obsolete_heartc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000442

The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions
Source
http://en.wikipedia.org/wiki/Heart
Example
Alan Ruttenberg's heart
has super-classes
Obsolete Class c

obsolete_identificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000446

a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
Example
DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
has super-classes
Obsolete Class c

obsolete_identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000128

has super-classes
Obsolete Class c

obsolete_immortal cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100035

a cell derived from a multicellular organism that has the potential to replicate indefinitely
Source
GROUP: OBI Biomaterial Branch
Example
a single Hela cell
has super-classes
Obsolete Class c

obsolete_immortal cell line culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100056

A cell line that is expected to be capable of indefinite propagation in an vitro culture.
Source
PERSON:Matthew Brush
has super-classes
Obsolete Class c

obsolete_label rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000140

Label role is a role which inheres in a material entity and which is realized in a detection of label assay
Source
OBI
has super-classes
Obsolete Class c

obsolete_left handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000937

has super-classes
Obsolete Class c

obsolete_liverc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302743

liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates
Source
GROUP: OBI Biomaterial Branch
Example
PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93.
has super-classes
Obsolete Class c

obsolete_material access provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000936

a service provider role which is realized by a servicer provider organization performing access to some material
Source
OBI
Example
A person or organization who provides access to a DNA sequencer.
has super-classes
Obsolete Class c

obsolete_material_entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000018

has super-classes
Obsolete Class c

obsolete_molecular concentrationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000577

A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity.
Source
Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
Example
the phosphate concentration should be 0.1M
has super-classes
Obsolete Class c

obsolete_occurrence of diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110002

An occurrence of disease is a process involving pathologic changes within an organism
Source
IEDB
has super-classes
Obsolete Class c

obsolete_peritoneumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000323

is the serous membrane that forms the lining of the abdominal cavity
has super-classes
Obsolete Class c

obsolete_platformc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000050

A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
Source
OBI Instrument branch
has super-classes
Obsolete Class c

obsolete_polymerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100069

A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
Source
TERM: CHEBI:33839
has super-classes
Obsolete Class c

obsolete_primary structure of proteinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000797

The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together
replaced by SO_0000104 polypeptide
Example
SIINFEKL' is the primary structure of a peptide
has super-classes
Obsolete Class c

obsolete_primary structure of sequence macromoleculec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000830

A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds
replaced by SO_0000001 region
has super-classes
Obsolete Class c

obsolete_protocol service provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000980

a service provider role which is realized by a servicer provider organization performing a protocol execution
Example
DNA sequencing of a sample by a core lab which returns data to the consumer
has super-classes
Obsolete Class c

obsolete_qualitative binding detection assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001009

A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context.
has super-classes
Obsolete Class c

obsolete_report elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000091

A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
Source
GROUP:OBI
OBI_0000001
has super-classes
Obsolete Class c

obsolete_report tablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000097

A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
Source
group:OBI
OBI_0000265
has super-classes
Obsolete Class c

obsolete_right handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000974

has super-classes
Obsolete Class c

obsolete_role of being first subject treatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000100

First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study
Source
OBI
Example
Rat 1A; first enrolled patient to receive treatment
has super-classes
Obsolete Class c

obsolete_sample populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000264

A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers.
Source
GROUP: OBI Biomaterial Branch
Example
Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458
has super-classes
Obsolete Class c

obsolete_specimen fixation functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001037

A specimen fixation function is a function that holds or fastens an entity in a fixed position.
duplicate term
has super-classes
Obsolete Class c

obsolete_study interpretationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000035

A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
Source
OBI_0000005
has super-classes
Obsolete Class c

obsolete_study resultc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000682

Study result is an information content entity that is a specified data output of a study.
Source
GROUP: OBI
has super-classes
Obsolete Class c

obsolete_survival curvec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000182

A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
Source
WEB: http://www.graphpad.com/www/book/survive.htm
has super-classes
Obsolete Class c

obsolete_training service provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000929

a service provider role which is realized by a servicer provider organization performing some training
Source
OBI
Example
EBI provides training on databases and tools and has a training service provider role
has super-classes
Obsolete Class c

obsolete_trypsinized materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000420

A material entity that has undergone a process of digestion with trypsin
Example
A trypsinized suspension of cells
has super-classes
Obsolete Class c

obsolete_unit of measurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000024

a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
Source
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
Example
The length of a ruler.
has super-classes
Obsolete Class c

occurrence of allergyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110012

The process of an allergic disease occurring in an organism.
Source
IEDB
is equivalent to
realizes op some allergy c
has super-classes
disease course c
has part op some allergic reaction c

occurrence of infectious diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110008

Is an occurrence of a disease caused by an infection
Source
IEDB
is equivalent to
realizes op some infectious disease c
has super-classes
disease course c
has part op some infection process c and (realizes op some disposition to infect an organism c)
immediately preceded by op some host exposure to infectious agent c

occurrentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000003

An entity that has temporal parts and that happens, unfolds or develops through time.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
entity c
has sub-classes
process c, process boundary c, spatiotemporal region c, temporal region c
is in domain of
has participant op, occurs in op, preceded by op, precedes op, process is result of op
is in range of
participates in op, preceded by op, precedes op, process is result of op, temporal relation op
is disjoint with
continuant c

OH-radical structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001029

a single-nucleotide-resolution nucleic acid structure mapping assay which uses hydroxyl radical as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:2501870
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some hydroxyl c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

oil bathc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400157

An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample).
Source
PERSON: Daniel Schober
Example
An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period.
has super-classes
temperature control bath c

oligonucleotide synthesizerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400113

An instrument used to chemically synthesize oligonucleotides.
Source
MO
Example
Automated Multiplex Oligonucleotide Synthesizer
has super-classes
physical store c
has function op some synthesizing function c
has function op some environment control function c
has sub-classes
DNA synthesizer c

Oncostatin M productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0044808

The appearance of Oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

one dimensional cartesian spatial coordinate datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000401

A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
has super-classes
cartesian spatial coordinate datum c
denotes op some zero-dimensional spatial region c and (part of op some one-dimensional spatial region c)
has x coordinate value dp exactly 1

one-dimensional continuant fiat boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000142

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
has super-classes
continuant fiat boundary c
is disjoint with
two-dimensional continuant fiat boundary c, zero-dimensional continuant fiat boundary c

one-dimensional spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000026

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
an edge of a cube-shaped portion of space.
has super-classes
spatial region c
is disjoint with
two-dimensional spatial region c, zero-dimensional spatial region c, three-dimensional spatial region c

one-dimensional temporal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000038

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
the temporal region during which a process occurs.
has super-classes
temporal region c
is disjoint with
zero-dimensional temporal region c

open tubular columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000606

An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube.
Source
WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219
has super-classes
chromatography column c

operational taxonomic unit matrixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001968

Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism.
Source
PRS for OBI
Example
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1610290/
has super-classes
data item c
is about op some material entity c
is_specified_output_of op some data transformation c

operator variation designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001195

A study design that assesses the operator performance and relation to data consistency and quality.
Source
MO_519 operator_variation_design
has super-classes
study design c
has part op some study design independent variable c and (is about op some Homo sapiens c and (has role op some worker role c))

operon identification designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001432

A study design that identifies locations and members of operons in a genome.
Source
MO_772 operon_identification_design
has super-classes
study design c
has part op some sequence feature identification objective c

Opisthokontac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_33154

has super-classes
Eukaryota c
has sub-classes
Ascomycota c, Bilateria c

opsonizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0008228

The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
has super-classes
phagocytosis c
has sub-classes
B cell epitope specific opsonization c

optical filterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400079

An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
Source
http://en.wikipedia.org/wiki/Optical_filter
Example
720 LP filter, 580/30 BP filter
has super-classes
material separation device c
has function op some filter function c
has sub-classes
band pass filter c, dichroic filter c, dichroic mirror c, long pass filter c, short pass filter c

optical microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000940

A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range
has super-classes
microscope c
has sub-classes
stereo microscope c

optical subsystemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400080

a device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles.
Source
John Quinn
Example
optical subsystem of a cytometer
has super-classes
device c
has part op some light source c
has part op some obscuration bar c
has part op some optical filter c

oral administrationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000952

The administration of a substance into the mouth of an organism
is equivalent to
(realizes op some material to be added role c) and (realizes op some target of material addition role c and (role of op some mouth c))
has super-classes
administering substance in vivo c
achieves_planned_objective op some adding material objective c
has sub-classes
oral ingestion of pill c

oral ingestion of pillc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000837

An adding a material entity to target with the entity is a pill and the target is the mouth
is equivalent to
(realizes op some material to be added role c and (role of op some pill c)) and (realizes op some target of material addition role c and (role of op some mouth c)) and (has_specified_input op some pill c)
has super-classes
oral administration c

organ harvestingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110046

The process of removing an organ from its source organism
Source
IEDB
has super-classes
material component separation c

organ sectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100066

A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
Source
GROUP: CEBS
GROUP: OBI Biomaterial Branch
Example
A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
has super-classes
processed material c
is_specified_output_of op some histological sample preparation c or collecting specimen from organism c
derives from op some material anatomical entity c

organellar RNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000899

A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
Source
UPenn Group
Example
Extraction of organellar RNA from plant cells using organellar RNA binding protein.
has super-classes
RNA extract c
is_specified_output_of op some organellar RNA extraction c

organellar RNA extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000849

A RNA extraction process in which the desired output material is RNA in the organelle(s).
Source
UPenn Group
has super-classes
RNA extraction c

organic acid columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000465

An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099
has super-classes
chromatography column c

organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100026

A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
Source
WEB: http://en.wikipedia.org/wiki/Organism
Example
animal
fungus
plant
virus
is equivalent to
Viruses c or Bacteria c or Archaea c or Eukaryota c
has super-classes
material entity c
has sub-classes
Archaea c, Bacteria c, Eukaryota c, Viruses c, chimera c, genetically modified organism c, host of immune response c, infectious agent c, selectively maintained organism c

organism development designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001328

A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
Source
MO_892 development_or_differentiation_design
has super-classes
study design c
has part op some organism feature identification objective c and (is about op some life cycle stage c and (has participant op some organism c))

organism feature identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000268

Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
has super-classes
biological feature identification objective c

organism identification assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001624

An assay that identifies the organism species in a specimen.
Source
NIAID GSCID-BRC metadata working group
is equivalent to
assay c and (achieves_planned_objective op some organism identification objective c)
has super-classes
assay c
(has_specified_input op some specimen c and (has part op some organism c)) and (has_specified_output op some information content entity c and (is about op some organism c))

organism identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001623

A biological feature identification objective to identify the organism species in a specimen.
Source
Penn Group
has super-classes
biological feature identification objective c

organism part comparison designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001422

A study design that compares tissues, regions, organs within or between organisms
Source
MO_953 organism_part_comparison_design
has super-classes
study design c
has part op some organism feature identification objective c
has part op some study design independent variable c and (is about op some material anatomical entity c)

organism status comparison designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001377

A study design that compares samples from live and dead organisms.
Source
MO_841 organism_status_design
has super-classes
study design c
has part op some biological feature identification objective c
is concretized as op some realized in op some assay c and (has_specified_input op some pre-mortem specimen c or post mortem specimen c)

organism substancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000463

Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
has super-classes
material anatomical entity c
has sub-classes
amniotic fluid c, bile c, blood c, cerebrospinal fluid c, digestive system fluid or secretion c, feces c, milk c, pericardial fluid c, peritoneal fluid c, pleural fluid c, saliva c, sputum c, sweat c, synovial fluid c, urine c, vitreous humor c

organismal qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001995

A quality that inheres in an entire organism or part of an organism.
has super-classes
quality c
has sub-classes
biological sex c

organizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000245

An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
Source
GROUP: OBI
Example
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has super-classes
material entity c
has sub-classes
Bioinformatics Resource Center c, grant agency c, hospital c, organization of Bioinformatics Resource Center contact person c, organization of sequencing facility contact person c, organization of specimen collector c, organization of specimen provider principal investigator c, regulatory agency c, research organization c, sequencing facility organization c, specimen repository organization c
is in domain of
has organization member op
is in range of
is member of organization op
has members
AES Chemunex ni, Advanced Instruments Inc. (AI Companies) ni, Affymetrix ni, Agilent ni, Ambion ni, Antigenix ni, Apogee Flow Systems ni, Applied Biosystems ni, BIO-RAD ni, Beckman Coulter ni, Becton Dickinson (BD Biosciences) ni, Bentley Instruments ni, Bruker Corporation ni, Bruker Daltonics ni, CytoBuoy ni, Cytopeia ni, Dako Cytomation ni, Exalpha Biological ni, Exbio Antibodies ni, Helicos ni, Illumina ni, Invitrogen ni, Li-Cor ni, Luminex ni, Millipore ni, Miltenyi Biotec ni, NanoString Technologies ni, Nimblegen ni, Pacific Biosciences ni, Partec ni, Roche ni, Sysmex Corporation, Kobe, Japan ni, Thermo ni, U.S. Food and Drug Administration ni, Waters ni, eBioscience ni

organization of Bioinformatics Resource Center contact personc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001881

An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center
Source
NIAID GSCID-BRC metadata working group
is equivalent to
organization c and (has organization member op some Bioinformatics Resource Center contact person c)
has super-classes
organization c

organization of sequencing facility contact personc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001897

An organization that is the affiliation of the contact representative at the sequencing facility
Source
NIAID GSCID-BRC metadata working group
is equivalent to
organization c and (has organization member op some sequencing facility contact person c)
has super-classes
organization c

organization of specimen collectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001893

An organization that is the affiliation of the person collecting the specimen
Source
NIAID GSCID-BRC metadata working group
is equivalent to
organization c and (has organization member op some specimen collector c)
has super-classes
organization c

organization of specimen provider principal investigatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001880

An organization that is the affiliation of the principal investigator providing the specimens for the investigation
Source
NIAID GSCID-BRC metadata working group
is equivalent to
organization c and (has organization member op some specimen provider principal investigator c)
has super-classes
organization c

oscilloscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000948

A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis).
Source
http://en.wikipedia.org/wiki/Oscilloscope
has super-classes
measurement device c
has function op some measure function c

ozone-induced chemiluminescence detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000598

Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry.
Source
WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088
has super-classes
gas chromatography detector c

p-valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000175

A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
Source
WEB: http://en.wikipedia.org/wiki/P-value
Example
PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
has super-classes
quantitative confidence value c

P815 cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110118

A cell line derived from mouse mastocytoma.
Source
IEDB
http://www.biotech.ist.unige.it/cldb/cl5244.html
has super-classes
immortal cell line c

PacBio RS IIc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002012

A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.
Source
http://www.pacificbiosciences.com/products/
Example
Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882
has super-classes
DNA sequencer c
is_manufactured_by op value Pacific Biosciences

packed columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000448

A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube.
Source
WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218
has super-classes
chromatography column c

paired-end libraryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000722

is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
Source
adapted from information provided by Solid web site
Example
PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
has super-classes
processed material c

paired-end library preparationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001852

A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.
Source
Venkat Malladi, Jie Zheng
is equivalent to
library preparation c and (has_specified_output op some paired-end library c)
has super-classes
library preparation c

pancreasc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001264

An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
has super-classes
material anatomical entity c

pancreas specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002527

A specimen that is derived from pancreas.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some pancreas c))
has super-classes
specimen from organism c

Pancrustaceac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_197562

has super-classes
Ecdysozoa c
has sub-classes
Daphnia c, Drosophila melanogaster c

paraffin ovenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001111

A device that is used for the warming of paraffin embedding medium.
Source
PERSON: Erik Segerdell
has super-classes
container c
environmental control device c
has function op some contain function c
has function op some heat function c
has function op some mechanical function c

paraffin specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000950

a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
Source
MO_990 paraffin_sample
Example
liver tissue embedded in paraffin
is equivalent to
(is_specified_output_of op some paraffin storage c and (has_specified_input op some has role op some specimen role c)) and (has role op some specimen role c)
has super-classes
specimen with known storage state c
is disjoint with
frozen specimen c, lyophilized specimen c, fresh specimen c, agar stab specimen c

paraffin storagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000977

a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
need to specify paraffin or wax is one of specified input of the process
Source
UPenn Group
Example
has super-classes
storage c
has_specified_input op some organism c or material anatomical entity c
achieves_planned_objective op some material maintenance objective c

parallel analysis of RNA structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002032

A single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution.
Source
pmid:20811459
Example
pmid:20811459
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c

parallel group designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500006

A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
Source
http://www.holah.karoo.net/experimentaldesigns.htm
Example
PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
has super-classes
study design c

parameter thresholdc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000172

A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role
Source
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
Example
0.01, 0.03
has super-classes
measurement datum c

pareto scalingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200037

A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable.
Source
PMID:16762068
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

partial least square discriminant analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200107

PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information.
Source
WEB: http://www.camo.com/rt/Resources/pls-da.html
has super-classes
discriminant analysis c

partial least square regression analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200105

Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that Y = b0 + b1X1 + b2X2 + ... + bpXp In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data.
Source
ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263.
has super-classes
regression analysis method c

participant under investigation rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000097

A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
Source
OBI
Example
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has super-classes
role c
realized in op only study design execution c
has sub-classes
reference subject role c, to be treated with active ingredient role c, to be treated with placebo role c

particle delivery vesselc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400081

Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
FC 500 particle delivery vessel
has super-classes
processed material c
has sub-classes
multi-well plate c

partitioning data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200171

A partitioning data transformation is a data transformation that has objective partitioning.
Source
PERSON: James Malone
is equivalent to
achieves_planned_objective op some partitioning objective c
has super-classes
data transformation c
has sub-classes
canonical variate analysis c, gating c, k-means clustering c, k-nearest neighbors c, statistical model validation c

partitioning objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200172

A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
Source
PERSON: Elisabetta Manduchi
Example
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
has super-classes
data transformation objective c
has sub-classes
cross validation objective c

passive immunizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001174

The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens.
Example
Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another.
has super-classes
administering substance in vivo c
realizes op some material to be added role c and (inheres in op some adaptive immune receptor c)
has sub-classes
epitope specific immune intervention c

patch clamp devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001080

A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
Source
http://en.wikipedia.org/wiki/Patch_clamp
has super-classes
measurement device c
has function op some measure function c

patentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000313

A document that has been accepted by a patent authority
Example
US Patent 6,449,603
has super-classes
document c

pathogen challengec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000712

A pathogen challenge is the administration of a live pathogenic organism to a host
has super-classes
administering substance in vivo c
realizes op some host role c
realizes op some material to be added role c and (role of op some organism c and (has role op some pathogen role c))
realizes op some target of material addition role c and (role of op some organism c and (has role op some host role c))

pathogen release in laboratory accidentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110019

a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent
Source
IEDB
has super-classes
environmental proximity to infectious agent c

pathogen rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000718

pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role
Source
OBI
Example
Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383
has super-classes
role c
inheres in op some organism c
realized in op only disease course c

pathogenicity designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001454

A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
Source
MO_807 pathogenicity_design
has super-classes
study design c
has part op some biological feature identification objective c

pathologic processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110122

abnormal, harmful processes caused by or associated with a disease
Source
IEDB
has super-classes
biological_process c
has sub-classes
allergic reaction c, infection process c

pathologist rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000145

a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline
has super-classes
worker role c

patient rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000093

a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
Source
OBI, CDISC
Example
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
has super-classes
role c
inheres in op some Homo sapiens c

pattern matching objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000868

A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees.
Source
http://en.wikipedia.org/wiki/Pattern_matching
has super-classes
data transformation objective c

PCR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000989

A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
has super-classes
thermal cycler c
has function op some realized in op only polymerase chain reaction c
has sub-classes
real-time PCR machine c

PCR productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000406

is double stranded DNA that is the specified output of a polymerase chain reaction
Source
GROUP: OBI BIomaterial Branch
Example
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
is equivalent to
double-stranded DNA c and (is_specified_output_of op some polymerase chain reaction c)
has super-classes
double-stranded DNA c
amplified DNA c

PCR programc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001961

a PCR program is a plan specification which is executed during a polymerase chain reaction (PCR) by a thermocycler instrument that will iterate through the changes in temperature and duration of each of the annealing, denaturation, elongation steps for as many times as specified by the program.
Source
OBI
Example
https://www.neb.com/protocols/1/01/01/taq-dna-polymerase-with-standard-taq-buffer-m0273
has super-classes
plan specification c

PCR-SSCP assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302737

a PCR-SSCP assay is an assay that identifies DNA sequence variation (mutation, deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure.
Source
PMID: 18219595.Mol Biotechnol. 2008 Feb;38(2):155-63.PCR-SSCP: a method for the molecular analysis of genetic diseases.
Example
PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene?
has super-classes
genotyping assay c
has part op some polymerase chain reaction c
has part op some material component separation c
has_specified_input op some amplified DNA c
has_specified_output op some image c
has_specified_output op some genotype information c
achieves_planned_objective op some assay objective c
has participant op some polyacrylamide gel c

PDB filec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001525

A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned.
Example
The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4
has super-classes
3D structural organization datum c

PDB file chainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001596

A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities
Source
IEDB
Example
The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex
has super-classes
3D structural organization datum c
part of op some PDB file c

peak matchingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000726

Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
Source
PERSON: Ryan Brinkman
has super-classes
data transformation c
has members
GenePattern peak matching ni

pearson correlation coefficient calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200115

A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered.
Source
PERSON: Elisabetta Manduchi
WEB: http://en.wikipedia.org/wiki/Correlation
has super-classes
similarity calculation c

peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16670

Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
has super-classes
macromolecule c
has sub-classes
protein c, synthetic peptide c

peptide antigen bindingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0042605

Interacting selectively and non-covalently with an antigen peptide.
has super-classes
antigen binding c

peptide constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1000042

a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion
Source
IEDB
Example
Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617
has super-classes
processed material c
has part op some peptide c
is_specified_output_of op some enzymatic ligation c

peptide mass fingerprintingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002035

A mass spectrometry assay in which an unknown protein of interest is cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer. These masses are then compared to values in a database containing known protein sequences.
Source
ERO:0001668 (http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting)
has super-classes
mass spectrometry assay c

perforin productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0035944

The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
biological_process c
has sub-classes
epitope specific perforin production by T cells c

performing a clinical assessmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600003

a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition.
Source
OBI branch derived
has super-classes
assay c
has part op some performing a diagnosis c
has_specified_input op some organism c and (has role op some patient role c)
has_specified_output op some diagnosis textual entity c
achieves_planned_objective op some assay objective c

performing a diagnosisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000988

The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
Example
Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache.
has super-classes
data transformation c
has_specified_output op some diagnosis textual entity c

perfusion stationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001067

A device or system in which perfusion units are integrated.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some specimen fixation function c

pericardial fluidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002409

Transudate contained in the pericardial cavity.[FMA]
has super-classes
organism substance c

pericardial fluid specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002506

A specimen that is derived from pericardial fluid.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some pericardial fluid c))
has super-classes
specimen from organism c

peritoneal fluidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001268

Transudate contained in the peritoneal cavity.
has super-classes
organism substance c

peritoneal fluid specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002514

A specimen that is derived from peritoneal fluid.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some peritoneal fluid c))
has super-classes
specimen from organism c

peritoneumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002358

A serous membrane that lines the peritoneal cavity[VHOG,modified].
has super-classes
multi-tissue structure c

perturb functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000377

A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
Source
http://en.wikipedia.org/wiki/Perturbation_biology
has super-classes
function c

perturbation devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001033

A perturbation device is a device which is designed to perform a perturb function
Source
OBI Vancouver workshop 2010
PERSON: Helen Parkinson
Example
A homogenizer is a perturbation device.
is equivalent to
has function op some perturb function c
has super-classes
device c
has sub-classes
homogenizer c, piezo electric crystal c, sonicator c, vortexer c

PET synthesizerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001054

A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some synthesizing function c

pH indicator dye rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000110

the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity
Example
phenol red in RPMI; pH=4 indicator dye (also carries reference role)
bromophenol blue has a pH indicator dye role
has super-classes
dye role c

pH meterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001047

A device that is used to measure the pH (acidity or alkalinity) of a liquid.
Source
http://en.wikipedia.org/wiki/PH_meter
has super-classes
measurement device c
has function op some measure function c

phage display assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001655

A B cell epitope qualitative binding to antibody assay that uses a phage display binding assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some phage display binding assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

phage display binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001476

A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner.
Source
IEDB
Example
Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated.
is equivalent to
binding assay c and (has part op some phage display library panning c) and (has part op some sequencing assay c) and (has_specified_input op some phage display library c)
has super-classes
binding assay c

phage display libraryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1000029

a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
Source
WEB: http://www.immuneepitope.org/home.do
Example
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
has super-classes
recombinant vector c
is_specified_output_of op some recombinant vector cloning c
has grain op some recombinant vector c

phage display library panningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001480

Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection.
Source
IEDB, http://en.wikipedia.org/wiki/Phage_display
Example
Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind.
has super-classes
material processing c
has_specified_input op some phage display library c

phagocytosisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0006909

An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
has super-classes
biological_process c
has sub-classes
opsonization c

phenol redc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_31991

3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney.
has super-classes
molecular entity c

phenotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000023

A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
has super-classes
quality c

phosphate buffered saline solutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100046

Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic).
Source
WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline
Example
PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes.
has super-classes
chemical solution c
has part op some scattered molecular aggregate c and (has grain op only sodium chloride c)
has part op some scattered molecular aggregate c and (has grain op only sodium phosphate c)
has role op some buffer role c

phosphorus-32 atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_37972

The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
has super-classes
atom c
has role op some molecular label role c

phosphorus-33 atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_37973

The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
has super-classes
atom c
has role op some molecular label role c

photodetectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400082

A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
Source
http://einstein.stanford.edu/content/glossary/glossary.html
Example
A photomultiplier tube, a photo diode
has super-classes
measurement device c
has function op some measure function c
has sub-classes
photodiode c

photodiodec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400083

A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer.
Source
http://cyto.mednet.ucla.edu/Protocols/flow.htm
Example
Avalanche photodiode
has super-classes
photodetector c
has sub-classes
avalanche photodiode c

photographc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000185

A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
Source
WEB: http://en.wiktionary.org/wiki/photograph
has super-classes
image c

photographic printc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000186

A photographic print is a material entity upon which a photograph generically depends.
is equivalent to
material entity c and (bearer of op some concretizes op some photograph c)
has super-classes
material information bearer c

photoionization detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000506

The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis.
Source
WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090
has super-classes
gas chromatography detector c

photomultiplier tubec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400084

A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect.
Source
http://cyto.mednet.ucla.edu/Protocols/flow.htm
Example
R9647 by manufactured by Hamamatsu
has super-classes
measurement device c
container c
has function op some contain function c
has function op some signal amplification function c
has function op some measure function c

physical documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000044

A physical document is an object serving as a record of information by means of symbolic marks.
Source
GROUP: OBI
Example
a book is a physical document
has super-classes
processed material c

physical storec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002089

A container with an environmental control function.
Source
Duke Biobank, OBIB
Example
a freezer. a humidity controlled box.
is equivalent to
has function op some environment control function c
has super-classes
container c
environmental control device c
has sub-classes
Faraday cage c, bioreactor c, chromatography device c, fluid pressure regulator c, gel dryer c, gel tank c, hybridization chamber c, hybridization station c, incubator c, incubator shaker c, isoelectric focusing device c, microarray platform c, microarray wash station c, molecular crosslinker c, oligonucleotide synthesizer c, sheath tank c, temperature control bath c, thermal cycler c, thermostatic circulator c, vacuum dryer c, vibration isolation table c

piezo electric crystalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400085

Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell.
Source
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
Example
quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar
has super-classes
perturbation device c
has function op some perturb function c

pillc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000827

A dose of medicine or placebo in the form of a small pellet.
Source
http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n
has super-classes
processed material c
has sub-classes
filled capsule c

piston-sealc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000568

The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless.
Source
WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116
has super-classes
chromatography consumable c

pituitary glandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000007

The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
has super-classes
material anatomical entity c

pituitary gland specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002529

A specimen that is derived from pituitary gland.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some pituitary gland c))
has super-classes
specimen from organism c

placebo rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000169

a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance
Example
Pill consisting of inert materials
has super-classes
negative reference substance role c

placentac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001987

organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
has super-classes
material anatomical entity c

placenta specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002513

A specimen that is derived from placenta.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some placenta c))
has super-classes
specimen from organism c

planc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000260

A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
Source
branch derived
Example
The plan of researcher X to perform an experiment according to a protocol.
has super-classes
realizable entity c

plan specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000104

A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
Source
OBI Plan and Planned Process branch
OBI_0000344
Example
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has super-classes
directive information entity c
has part op some objective specification c
has part op some action specification c
has sub-classes
PCR program c, algorithm c, grant c, investigation assay specification c, programming language c, protocol c, software c, software pipeline c, specimen-based scope of investigation specification c, study design c, target capture specification c, target material in specimen specification c

planned processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000011

A processual entity that realizes a plan which is the concretization of a plan specification.
Source
branch derived
Example
Injecting mice with a vaccine in order to test its efficacy
is equivalent to
realizes op some concretizes op some plan specification c
has super-classes
process c
has sub-classes
animal feeding c, assay c, assigning a centrally registered identifier c, associating information with a centrally registered identifier in its registry c, calibration c, comparing prediction to measurement c, data item extraction from journal article c, data transformation c, data visualization c, document editing c, documenting c, drawing a conclusion c, drawing a conclusion based on data c, exposure of material to environment c, freezing c, group assignment c, image creation c, informed consent process c, informing investigator of subject study arm c, informing subject of study arm c, investigation c, laboratory animal care c, looking up a centrally registered identifier c, material maintenance c, material processing c, prediction c, presentation of stimulus c, selection c, sequence annotation c, service c, specimen collection process c, study design execution c, study intervention c, subject agrees they understand informed consent document c, supplying c, training process c, treatment c, treatment portion of study execution c, unblinding process c, validation c
is in domain of
achieves_planned_objective op, has performer op, has_specified_input op, has_specified_output op
is in range of
is_specified_input_of op, is_specified_output_of op, objective_achieved_by op
is disjoint with
biological_process c

planningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000339

a process of creating or modifying a plan specification
Source
Bjoern Peters
Plans and Planned Processes Branch
Example
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
has super-classes
process c
process c and (has participant op some plan specification c)
is disjoint with
assay c

plasma cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000786

A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
has super-classes
B cell c

plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000430

plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
Source
group:OBI
is equivalent to
double-stranded DNA c and (has function op some realized in op only gene expression c) and (has quality op some circular c)
has super-classes
double-stranded DNA c
has sub-classes
cloning plasmid c, recombinant plasmid c

plasmon resonance assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001651

A B cell epitope qualitative binding to antibody assay that uses a surface plasmon resonance assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some surface plasmon resonance binding assay c)
has super-classes
assay measuring qualitiative binding of a B cell epitope:antibody complex c

plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001229

A T cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex c and (has part op some surface plasmon resonance binding assay c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex c

plate loaderc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400086

Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications.
Source
http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf
Example
FC 500 plate loader
has super-classes
device c
has function op some transfer function c

plate shakerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001094

A device that provides shaking motion for microplates.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some mechanical function c

platelet activating factor productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0002390

The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

pleural fluidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001087

Transudate contained in the pleural cavity.
has super-classes
organism substance c

pleural fluid specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002515

A specimen that is derived from pleural fluid.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some pleural fluid c))
has super-classes
specimen from organism c

ploidyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001374

A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
has super-classes
cellular quality c
has sub-classes
aneuploid c, diploid c, haploid c, polyploid c

plunger columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000586

A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108
has super-classes
chromatography column c

podzolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_00002257

Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.
has super-classes
soil c

poly(A)-site sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002045

A RNA-seq assay for quantitatively profiling RNA polyadenylation at the transcriptome level.
Source
Shepard et al., (April 2011). "Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq." RNA. 2011 Apr;17(4):761-72. doi: 10.1261/rna.2581711
Example
Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615.
has super-classes
RNA-seq assay c

polyA RNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000869

A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
Source
UPenn Group
Example
Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
has super-classes
RNA extract c
is_specified_output_of op some polyA RNA extraction c

polyA RNA extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000848

A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
Source
UPenn Group
has super-classes
RNA extraction c

polyacrylamide gelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000432

a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
Source
GROUP: OBI Biomaterial Branch
Example
Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
has super-classes
processed material c
has part op some acrylamide c
is_specified_output_of op some polymerization c

polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl etherc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000065

triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties
Source
adapted from Wikipedia before possible import from CHEBI
Example
PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
has super-classes
molecular entity c

polymerase chain reactionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000415

PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
Source
adapted from wikipedai
Example
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
has super-classes
enzymatic amplification c
realizes op some synthesizing function c and (inheres in op some DNA polymerase complex c)
has_specified_input op some deoxyribonucleic acid c
has_specified_output op some PCR product c
achieves_planned_objective op some material transformation objective c
has sub-classes
multiplex ligation-mediated amplification c

polymerizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302890

polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
Source
OBI-Branch
Example
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
has super-classes
material processing c
has_specified_input op some molecular entity c
has_specified_output op some macromolecule c
achieves_planned_objective op some material transformation objective c

polynomial degreec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200152

The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
Source
PERSON: Elisabetta Manduchi
has super-classes
mathematical feature c
has_feature_value dp some non negative integer

polynomial transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200093

A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
Source
WEB: http://mathworld.wolfram.com/Polynomial.html
Example
a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables
has super-classes
data transformation c
has sub-classes
homogeneous polynomial transformation c

polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000104

A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
has super-classes
region c

polyploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001377

A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
has super-classes
ploidy c

polystyrene tubec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000084

a polystyrene tube is a test tube made of polystyrene
Source
PERSON: Chris Stoeckert
Example
Polystyrene tubes can be used to contain tissue culture cells during centrifgation
has super-classes
test tube c

pool of specimensc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302716

A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
Source
GROUP: CEBS
is equivalent to
specimen c and (is_specified_output_of op some material combination c and (has_specified_input op only specimen c))
has super-classes
processed specimen c

pooling specimensc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600016

physical combination of several instances of like material
Source
OBI branch derived
Example
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
has super-classes
material combination c
has_specified_input op some specimen c
has_specified_output op some pool of specimens c
achieves_planned_objective op some material combination objective c
has_specified_input op min 2

populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000181

a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
Source
adapted from Oxford English Dictionnary
Example
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has super-classes
material entity c

portable fluorometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001120

A compact fluorometer that can be carried or moved with ease.
Source
PERSON: Erik Segerdell
has super-classes
fluorometer c

portioning objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000678

A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
Example
The objective to obtain multiple aliquots of an enzyme preparation.
has super-classes
material separation objective c
is disjoint with
separation into different composition objective c

positive reference substance rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000064

a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response
Example
MMS mutagen
has super-classes
reference substance role c
realized in op only assay c
has sub-classes
competitive binding reference ligand role c

positron emission tomography scannerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000933

A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule.
Source
http://en.wikipedia.org/wiki/Positron_emission_tomography
has super-classes
image creation device c
has function op some image acquisition function c

post mortem specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000902

a specimen that was taken from a dead organism
Source
MO_416 postmortem
Example
the spleen taken from a dead mouse
is equivalent to
is_specified_output_of op some specimen collection process c and (has_specified_input op some organism c and (has quality op some dead c))
has super-classes
specimen with pre- or post-mortem status c
is disjoint with
pre-mortem specimen c

post-transcriptional modification designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001358

A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases
Source
MO_392 cellular_modification_design
has super-classes
intervention design c
has part op some biological feature identification objective c
has part op some study design independent variable c and (is about op some study intervention c)

postal addressc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000422

A textual entity that is used as directive to deliver something to a person, or organization
has super-classes
textual entity c
is about op some geographic location c

power supplyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400142

A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
Source
PERSON: Daniel Schober
sep:00093
Example
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
has super-classes
device c
has function op some electricity supply function c

pre-mortem specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000873

a specimen that was taken from a live organism
Source
MO_705 premortem
Example
material obtained through a liver biopsy from a human patient
is equivalent to
is_specified_output_of op some specimen collection process c and (has_specified_input op some organism c and (has quality op some alive c))
has super-classes
specimen with pre- or post-mortem status c
is disjoint with
post mortem specimen c

preamplifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400087

A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
Built in preamplifier in a Hamamatsu H9656 PMT
has super-classes
voltage amplifier c

precipitatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000286

a precipitate is a material entity which is output of a precipitation process
Source
GROUP: OBI Biomaterial Branch
Example
Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038
has super-classes
processed material c
is_specified_output_of op some precipitation c

precipitationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600034

a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate)
Source
OBI branch derived
Example
The use of ethanol to precipitate DNA molecules from a solution containing DNA
has super-classes
material component separation c
achieves_planned_objective op some separation into different composition objective c

predicted data itemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302867

A data item that was generated on the basis of a calculation or logical reasoning
is equivalent to
is_specified_output_of op some prediction c
has super-classes
data item c

predicted mass valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001935

A predicted value where the prediction specifies the mass of some thing.
is equivalent to
predicted value c and (has part op some mass value specification c)
has super-classes
predicted value c

predicted valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001934

an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error.
has super-classes
information content entity c
has part op some value specification c
has part op some plan specification c and (concretizes op only realizes op some comparing prediction to measurement c)
has sub-classes
predicted mass value c

predictionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302910

a process by which an event or an entity is described before it actually happens or is being discovered and identified.
Source
OBI
Example
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190
has super-classes
planned process c
has_specified_input op some measurement datum c
has_specified_output op some measurement datum c

preparative autosamplerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000526

For preparative LC with injection of sample volumes ranging from L to mL ranges.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062
has super-classes
liquid chromatography autosampler c

preparative chromatographyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600046

the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
Source
OBI branch derived
Example
The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides.
has super-classes
material component separation c
has_specified_output op some eluate c
achieves_planned_objective op some separation into different composition objective c
has participant op some chromatography column c
has participant op some chromatography device c

presentation of stimulusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000807

a planned process in which an organism is exposed to some stimulus with the intent to invoke an action
Source
Helen Parkinson, Jessica Turner, Dirk Derom
Example
The presentation of a flashing light to a monkey during reward training
has super-classes
planned process c
has participant op some organism c and (has role op some participant under investigation role c)

pressurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001025

A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
has super-classes
quality of a single physical entity c

pressure unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000109

A unit which is a standard measure of the force applied to a given area.
has super-classes
measurement unit label c

primary cell culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001910

A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored.
Source
OBI-CLO Alignment Working Group (Spring 2013)
has super-classes
cell culture c
has part op some primary cultured cell c

primary cultured cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000001

A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
has super-classes
cultured cell c
not (is_specified_output_of op some cell culture splitting c)
not (derives from op some cultured cell c and (is_specified_output_of op some cell culture splitting c))

primary cultured cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100061

A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged.
Source
PERSON:Matthew Brush
Example
Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934
cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use)
has super-classes
cultured cell population c
has grain op some primary cultured cell c
has grain op only primary cultured cell c
is_specified_output_of op exactly 0 cell culture splitting c

primary structure of DNA macromoleculec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000811

a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
is equivalent to
is concretized as op some inheres in op some deoxyribonucleic acid c
has super-classes
region c

primary structure of RNA moleculec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000845

The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
is equivalent to
is concretized as op some inheres in op some ribonucleic acid c
has super-classes
region c

primer rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000405

a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.
Source
(cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer
has super-classes
complementary nucleotide probe role c
realized in op only polymerase chain reaction c

principal component regressionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200104

The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.
Source
WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html
has super-classes
regression analysis method c
class discovery data transformation c
(has_specified_output op some clustered data set c) and (achieves_planned_objective op some class discovery objective c)

principal components analysis dimensionality reductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200051

A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
has super-classes
dimensionality reduction c
has members
GenePattern PCA ni

principal investigator rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000103

a responsible party role played by a person responsible for the overall conduct of a study
has super-classes
responsible party role c

probabilistic algorithmc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200052

A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data.
Source
PERSON: James Malone
has super-classes
data transformation c
has sub-classes
expectation maximization c

processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000015

An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
has super-classes
occurrent c
has sub-classes
antigen binding c, biological_process c, history c, planned process c, planning c, process profile c, unplanned occurrence effecting an investigation c
is in domain of
realizes op
is in range of
is duration of op, realized in op
is disjoint with
temporal region c, spatiotemporal region c, process boundary c

process boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000035

p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
the boundary between the 2nd and 3rd year of your life.
has super-classes
occurrent c
is disjoint with
temporal region c, spatiotemporal region c, process c

process profilec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000144

b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
has super-classes
process c
is disjoint with
history c

processed materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000047

Is a material entity that is created or changed during material processing.
Example
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
is equivalent to
material entity c and (is_specified_output_of op some material processing c)
has super-classes
material entity c
has sub-classes
Berichrom(r) Antithrombin III (A) Kit c, Epstein Barr virus transformed B cell c, NTP-2000 c, agarose gel c, amplified DNA c, assay bead c, cell culture c, cell culture supernatant c, cell freezing medium c, cell lysate c, cell pellet c, cloning vector c, culture medium c, cultured cell population c, decapitated organism c, denatured polymer c, device c, eluate c, enzyme-linked antibody c, experimentally modified cell in vitro c, extract c, genetically modified material c, methylated polymer c, molecular-labeled material c, multiplexed sequencing library c, nucleic acid restriction enzyme digest c, organ section c, paired-end library c, particle delivery vessel c, peptide construct c, physical document c, pill c, polyacrylamide gel c, precipitate c, processed specimen c, purified material c, reagent c, recombinant vector c, screening library c, single fragment library c, synthetic peptide c, xenograft c

processed specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000953

A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
Source
Bjoern Peters
Example
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
is equivalent to
processed material c and specimen c
has super-classes
processed material c
specimen c
has sub-classes
blood plasma specimen c, blood serum specimen c, labeled specimen c, lymph node cell specimen c, nucleic acid extract c, pool of specimens c, splenocyte specimen c, whole mount tissue c

programmable array microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001071

A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures.
Source
Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8
has super-classes
confocal microscope c
has function op some measure function c

programming languagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000025

A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
Source
OBI_0000058
group:OBI
Example
R, Perl, Java
has super-classes
plan specification c

projectc back to ToC or Class ToC

IRI: http://usefulinc.com/ns/doap#Project

is defined by
http://usefulinc.com/ns/doap
has super-classes
thing c
has members
project ni, project ni

promoter activity detection by reporter gene assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000913

An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene.
Source
IEDB
Example
A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color.
has super-classes
binding assay c
has_specified_input op some cell c
has_specified_output op some is about op some core promoter binding c

promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001402

An assay of epitope specific interleukin-2 production by T cells that uses a promoter activity detection by reporter gene assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interleukin-2 production by T cells c and (has part op some promoter activity detection by reporter gene assay c)
has super-classes
biological activity assay measuring epitope specific interleukin-2 production by T cells c

proportion of expected false positives correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200164

A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses.
Source
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
has super-classes
multiple testing correction method c
(has_specified_output op some error corrected data set c) and (achieves_planned_objective op some multiple testing correction objective c)

proportional hazards model estimationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200195

Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system.
Source
WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model
has super-classes
survival analysis data transformation c
achieves_planned_objective op some survival analysis objective c

prostate glandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002367

The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
has super-classes
material anatomical entity c

prostate gland specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002518

A specimen that is derived from prostate gland.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some prostate gland c))
has super-classes
specimen from organism c

protease cleavagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600056

protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments).
Source
OBI branch derived
Example
the use of trypsin to cleave pepsin into peptide fragments
has super-classes
enzymatic cleavage c
has_specified_input op some protein c and (located in op some material entity c)
has_specified_output op some peptide c
has sub-classes
trypsination c

protection from challenge in vivo intervention experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001982

An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host.
Source
IEDB
Example
Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide.
has super-classes
in vivo intervention experiment c

proteinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000000001

An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
Example
antithrombin III is a protein
has super-classes
peptide c
has sub-classes
CD3 subunit with immunoglobulin domain c, CD4 molecule c, CD8 receptor c, DNA ligase c, T cell receptor co-receptor CD8 c, antithrombin-III c, deoxyribonuclease-1 c, double-stranded RNA-specific adenosine deaminase c, glial cell line-derived neurotrophic factor c, guanyl-specific ribonuclease T1 c, nuclease S1 c, restriction enzyme c, ribonuclease CL3 c, ribonuclease T2 c, ribonuclease U2 c, ribonuclease V1 c

protein and DNA interaction identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001398

A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
Source
MO_933 binding_site_identification_design
has super-classes
sequence feature identification objective c

protein and RNA interaction identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001854

A sequence feature identification objective that aims to characterize the interactions between protein and RNA.
Source
Jie Zheng
has super-classes
sequence feature identification objective c

protein binding site identification designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001425

A study design that investigates protein binding sites on nucleic acids.
Source
MO_933 binding_site_identification_design
is equivalent to
has part op some protein and DNA interaction identification objective c
has super-classes
study design c
has sub-classes
ChIP-chip design c, ChIP-seq design c

protein columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000468

A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
has super-classes
chromatography column c

protein complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0043234

Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
Example
A ribosome is a protein complex
has super-classes
material entity c
has part op some protein c
has sub-classes
DNA polymerase complex c, MHC protein complex c, adaptive immune receptor c, immunoglobulin complex c

protein domain specific bindingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0019904

Interacting selectively and non-covalently with a specific domain of a protein.
has super-classes
binding c

protein expression profilingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000615

a planned process which aims to provide information about protein expression and translation activity using protein extracts collected from a material entity using a range of techniques and instrument such as Mass spectrometers, Gel electrophoresis, Western Blots, Protein microarrays
Source
OBI branch derived
Example
Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. Finnegan S, Robson JL, Wylie M, Healy A, Stitt AW, Curry WJ. Proteome Sci. 2008 Dec 10;6(1):34.PMID: 19077203
has super-classes
assay c
achieves_planned_objective op some assay objective c

protein extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000894

a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation,
Source
OBI & wikipedia
Example
PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
has super-classes
extract c
has part op some protein c
is_specified_output_of op some extraction c

protein microarrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400149

A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
Source
PERSON: Daniel Schober
Example
The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
has super-classes
microarray c

protein separation apparatusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001082

A device that is used for the separation of proteins.
Source
PERSON: Erik Segerdell
has super-classes
material separation device c
has function op some material separation function c

protein sequencerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001137

An device that is used to determine the order of amino acids in protein sequences.
Source
PERSON: Erik Segerdell
has super-classes
measurement device c
has function op some measure function c

protein sequencing by tandem mass spectrometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001923

A sequencing assay in which amino acid sequences of proteins is determined using multiple rounds of mass spectrometry and molecule fragmentation.
Source
Hunt et al. Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1986;83(17): 6233–6237. [PMID:3462691]
Example
Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305]
has super-classes
sequencing assay c
has part op some protease cleavage c
realizes op some evaluant role c and (role of op some protein c)
has_specified_output op some sequence data c
has participant op some tandem mass spectrometer c

protein-protein interaction detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000288

An assay with the objective to determine interactions between proteins, such as protein-protein binding.
has super-classes
assay c

proteomic profiling by array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001318

An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
Source
EFO_0002765 proteomic profiling by array
has super-classes
analyte assay c
realizes op some analyte role c and (role of op some protein c)
has_specified_input op some specimen c and (has part op some protein c)
achieves_planned_objective op some molecular feature identification objective c
has participant op some protein microarray c

proteomic profiling by array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001441

A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
Source
Group: ArrayExpress production team
has super-classes
study design c
has part op some molecular feature identification objective c
is concretized as op some realized in op some (has part op some proteomic profiling by array assay c) and (has participant op some protein microarray c)

prothrombin time assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000802

The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma.
Source
WEB:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06
Example
PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
has super-classes
assay c
(has_specified_input op some blood serum specimen c) and (has_specified_output op some scalar measurement datum c and (is about op some blood coagulation c))

protocolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000272

A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
Source
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Example
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has super-classes
plan specification c
has sub-classes
animal care protocol c

protocol optimization designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001401

A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
Source
MO_934 optimization_design
has super-classes
study design c
has part op some protocol optimization objective c

protocol optimization objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000186

Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
has super-classes
protocol testing objective c

protocol testing objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000096

Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
has super-classes
methodology testing objective c
has sub-classes
protocol optimization objective c

protonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_24636

Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
has super-classes
molecular entity c

proxy respondent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000211

Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
has super-classes
worker role c

publicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000311

A document that has been accepted by a publisher
Example
A journal article or book
has super-classes
document c
has sub-classes
publication about an investigation c

publication about an investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000312

A publication that is about an investigation
Example
Most scientific journal articles
has super-classes
publication c
is about op some investigation c

PubMed IDc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001617

A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
Source
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
has super-classes
centrally registered identifier symbol c
denotes op exactly 1 publication c

pulsed amperometric detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000595

A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC).
Source
WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240
has super-classes
measurement device c
has function op some measure function c

pulsed-field gel electrophoresis systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001106

A gel electrophoresis system that is used to separate very large molecules of DNA.
Source
http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis
has super-classes
gel electrophoresis system c

pump functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001042

a transfer unction where the transfer requires work to move the entity, often against a gradient.
has super-classes
transfer function c

pump valve switchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000041

A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.
Source
OBI
has super-classes
device c
has function op some mechanical function c

purificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001505

A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
Source
MO_406 purify
is equivalent to
achieves_planned_objective op some purification objective c
has super-classes
material component separation c

purification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000796

The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
Source
BP
Example
the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
has super-classes
separation into different composition objective c

purified materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001633

A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component
Source
OBI conference call
Example
A mixture of peptide molecules that has been run through an HPLC column to remove 65
is equivalent to
material entity c and (is_specified_output_of op some purification c)
has super-classes
processed material c
has sub-classes
purified MHC molecule preparation c

purified MHC binding assay measuring binding of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001555

A MHC binding qualitative binding to ligand assay using MHC in a purified MHC molecule preparation.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a MHC:ligand complex c and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c))
has super-classes
assay measuring qualitiative binding of a MHC:ligand complex c
has sub-classes
purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection c, purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection c, purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection c, purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display c, purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection c

purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001534

A purified MHC binding assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
has super-classes
fluorescence detection binding assay c
purified MHC binding assay measuring binding of a MHC:ligand complex c
has part op some fluorescence detection assay c
has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)

purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001667

A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value.
Source
IEDB
has super-classes
purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection c
has part op some fluorescence detection assay c
has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)
has_specified_output op some has measurement unit label op value nanomolar

purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001564

A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value.
Source
IEDB
has super-classes
purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection c
has part op some radioactivity detection c
has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)
has_specified_output op some has measurement unit label op value nanomolar

purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001537

A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
fluorescence detection binding assay c
assay measuring the dissociation constant [KD] of a MHC:ligand complex c
has sub-classes
purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection c

purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001989

A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
radioactivity detection binding assay c
assay measuring the dissociation constant [KD] of a MHC:ligand complex c
has sub-classes
purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection c

purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001613

A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
fluorescence detection binding assay c
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c

purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001568

A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
is equivalent to
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
radioactivity detection binding assay c
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex c

purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001513

A purified MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
Source
IEDB
has super-classes
radioactivity detection binding assay c
purified MHC binding assay measuring binding of a MHC:ligand complex c
has part op some radioactivity detection c
has_specified_input op some material entity c and (has role op some competitive binding reference ligand role c)
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)

purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001604

A purified MHC binding assay that uses fluorescence detection to measure the 50% dissociation of binding temperature of direct ligand binding.
Source
IEDB
has super-classes
fluorescence detection binding assay c
purified MHC binding assay measuring binding of a MHC:ligand complex c
has part op some fluorescence detection assay c
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)
has_specified_output op some 50% dissociation of binding temperature (Tm) c
has_specified_output op some has measurement unit label op value degree Celsius

purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001590

A purified MHC binding assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
has super-classes
fluorescence detection binding assay c
purified MHC binding assay measuring binding of a MHC:ligand complex c
has part op some fluorescence detection assay c
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)

purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage displayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001584

A purified MHC binding assay that uses a phage display binding assay to measure direct ligand binding.
Source
IEDB
has super-classes
purified MHC binding assay measuring binding of a MHC:ligand complex c
has part op some phage display binding assay c
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)

purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001569

A purified MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the off rate measurement [koff] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value hertz)
has super-classes
fluorescence detection binding assay c
assay measuring the off rate measurement [koff] of a MHC:ligand complex c

purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001541

A purified MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value count per nanomolar second)
has super-classes
fluorescence detection binding assay c
assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex c

purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001543

A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to measure direct ligand binding and provides EC50 values determined under assay conditions where the EC50 approximates a KD value.
Source
IEDB
has super-classes
fluorescence detection binding assay c
assay measuring the dissociation constant [KD] of a MHC:ligand complex c
has part op some fluorescence detection assay c
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)
has_specified_output op some has measurement unit label op value nanomolar

purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001531

A purified MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the half life of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value minute)
has super-classes
fluorescence detection binding assay c
assay measuring the half life of a MHC:ligand complex c

purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001586

A purified MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the half life of a MHC:ligand complex c and (has part op some radioactivity detection c) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value minute)
has super-classes
radioactivity detection binding assay c
assay measuring the half life of a MHC:ligand complex c

purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001592

A purified MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding.
Source
IEDB
is equivalent to
assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex c and (has part op some fluorescence detection assay c) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
fluorescence detection binding assay c
assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex c

purified MHC direct binding assay of a MHC:ligand complex using radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001608

A purified MHC binding assay that uses radioactivity detection to measure direct ligand binding.
Source
IEDB
has super-classes
radioactivity detection binding assay c
purified MHC binding assay measuring binding of a MHC:ligand complex c
has part op some radioactivity detection c
has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)

purified MHC molecule preparationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001485

A mixture containing MHC molecules that was purified to remove non-MHC molecular entities.
Example
HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody
has super-classes
purified material c
(has part op some MHC protein complex c) and (is_specified_output_of op some purification c)

putamenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001874

Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion.
has super-classes
anatomical cluster c

pyrosequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000730

is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin.
Source
Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site
Example
Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review.
has super-classes
DNA sequencing by synthesis c
has participant op some 454 Genome Sequence 20 c or 454 Genome Sequencer FLX c

q-valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001442

A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
Source
Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
Example
PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
has super-classes
quantitative confidence value c

qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000019

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
has super-classes
specifically dependent continuant c
has sub-classes
device setting c, information carrier c, length c, mass c, mixed sex c, organismal quality c, phenotype c, quality of a single physical entity c, quality of related physical entities c, relational quality c
is in range of
has quality op, is quality measurement of op
is disjoint with
realizable entity c

quality control testing designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001336

A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
Source
MO_981 quality_control_testing_design
has super-classes
study design c

quality of a gasc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001547

A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
has super-classes
quality of a single physical entity c

quality of a liquidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001548

A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
has super-classes
quality of a single physical entity c

quality of a single physical entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001237

A physical object quality which inheres in a single-bearer.
has super-classes
quality c
has sub-classes
DNA residue methylation c, age c, alive c, behavioral quality c, biomaterial purity c, cellular quality c, circular c, damaged c, dead c, fluid flow rate c, frozen c, pressure c, quality of a gas c, quality of a liquid c, quality of a solid c, secondary structure of sequence macromolecule c, temperature c, volume c

quality of a solidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001546

A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
has super-classes
quality of a single physical entity c

quality of related physical entitiesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001238

A physical entity quality which exists in relation towards some other entity.
has super-classes
quality c
has sub-classes
diluted c, relational spatial quality c

quantile calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200118

A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details.
Source
WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html
has super-classes
descriptive statistical calculation data transformation c
achieves_planned_objective op some descriptive statistical calculation objective c

quantile number of false positives correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200161

A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed'
Source
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
has super-classes
multiple testing correction method c
(has_specified_output op some error corrected data set c) and (achieves_planned_objective op some multiple testing correction objective c)

quantile proportion of false positives correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200165

A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate).
Source
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
has super-classes
multiple testing correction method c
(has_specified_output op some error corrected data set c) and (achieves_planned_objective op some multiple testing correction objective c)

quantile transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200028

A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles.
Source
PERSON: Elisabetta Manduchi
Example
This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
has super-classes
normalization data transformation c
center calculation data transformation c
(has_specified_output op some center value c) and (achieves_planned_objective op some center calculation objective c)
achieves_planned_objective op some data normalization objective c

quantitative confidence valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000071

A data item which is used to indicate the degree of uncertainty about a measurement.
Source
group:OBI
has super-classes
data item c
has sub-classes
FWER adjusted p-value c, p-value c, q-value c, standard error c

quantitative node degree calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200131

A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node.
Source
PERSON: Richard Scheuermann
has super-classes
node quality calculation c

quantitative subgraph degree calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200139

A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph.
Source
PERSON: Richard Scheuermann
has super-classes
network subgraph quality calculation c

quartz cuvette flow chamberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400088

A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells.
Source
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
Example
CVF-Q-10 flow chamber, CV-Q-10 flow chamber
has super-classes
flow cell c

quaternary pump systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000627

A pump system that pump and mix up to four different solvents in parallel.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047
has super-classes
chromatography pump system c

quenching assay measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001726

A B cell epitope qualitative binding to antibody assay that uses an antibody binding detection by fluorescence quenching.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some antibody binding detection by fluorescence quenching c)
has super-classes
fluorescence detection binding assay c
assay measuring qualitiative binding of a B cell epitope:antibody complex c

quenching assay measuring the association constant [KA] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001732

A B cell epitope equilibrium association constant (KA) determination assay that uses an antibody binding detection by fluorescence quenching assay.
Source
IEDB
is equivalent to
assay measuring the association constant [KA] of a B cell epitope:antibody complex c and (has part op some antibody binding detection by fluorescence quenching c) and (has_specified_output op some has measurement unit label op value count per nanomolar)
has super-classes
fluorescence detection binding assay c
assay measuring the association constant [KA] of a B cell epitope:antibody complex c

quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001729

A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an antibody binding detection by fluorescence quenching assay.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c and (has part op some antibody binding detection by fluorescence quenching c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
fluorescence detection binding assay c
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c

quenching assay measuring the off rate [koff] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001740

A B cell epitope binding off rate measurement (koff) determination assay that uses an antibody binding detection by fluorescence quenching assay.
Source
IEDB
is equivalent to
assay measuring the off rate [koff] of a B cell epitope:antibody complex c and (has part op some antibody binding detection by fluorescence quenching c) and (has_specified_output op some has measurement unit label op value hertz)
has super-classes
fluorescence detection binding assay c
assay measuring the off rate [koff] of a B cell epitope:antibody complex c

quenching assay measuring the on rate [kon] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001742

A B cell epitope on rate measurement (kon) determination assay that uses an antibody binding detection by fluorescence quenching assay.
Source
IEDB
is equivalent to
assay measuring the on rate [kon] of a B cell epitope:antibody complex c and (has part op some antibody binding detection by fluorescence quenching c) and (has_specified_output op some has measurement unit label op value count per molar second)
has super-classes
fluorescence detection binding assay c
assay measuring the on rate [kon] of a B cell epitope:antibody complex c

questionnairec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001000

A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
Source
Merriam-Webster
has super-classes
document c
has members
Edingburgh handedness inventory ni

radiation measurement devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001086

A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector.
Source
PERSON: Erik Segerdell
has super-classes
measurement device c
has function op some record function c
has function op some measure function c

radio immuno assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000910

An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody.
Source
IEDB
Example
To evaluate the specificity of antibody binding to 35S-labeled IA-2(256‰ÛÒ760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256‰ÛÒ760) fragments were tested. Unlabeled recombinant IA-2(256‰ÛÒ760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4å¡C with patient sera. The following day, after incubation with radiolabeled 35S‰ÛÒIA-2(256‰ÛÒ760) or 35S‰ÛÒIA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay.
has super-classes
assay c
(realizes op some molecular label role c and (inheres in op some material entity c and (bearer of op some radioactive c))) and (has_specified_input op some material entity c and (bearer of op some radioactive c))
has part op some radioactivity detection c

radio immuno assay measuring epitope specific interferon-gamma production by T cellsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001433

An assay of epitope specific interferon-gamma production by T cells that uses a radio immuno assay.
Source
IEDB
is equivalent to
biological activity assay measuring epitope specific interferon-gamma production by T cells c and (has part op some radio immuno assay c)
has super-classes
biological activity assay measuring epitope specific interferon-gamma production by T cells c

radioactivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001741

A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
has super-classes
disposition c

radioactivity detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000201

An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material.
Source
IEDB
Example
Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material.
is equivalent to
assay c and (has_specified_input op some material entity c and (bearer of op some radioactive c)) and (has_specified_output op some is about op some realizes op some radioactive c)
has super-classes
assay c

radioactivity detection binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001491

binding assay that uses radioactivity detection as an indicator of binding
Source
IEDB
is equivalent to
binding assay c and (has part op some radioactivity detection c)
has super-classes
binding assay c
has sub-classes
RIA measuring binding of a B cell epitope:antibody complex c, RIA measuring the association constant [KA] of a B cell epitope:antibody complex c, RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex c, cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection c, cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection c, cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection c, cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection c, cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection c, cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection c, cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection c, cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection c, cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection c, cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection c, purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection c, purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection c, purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection c, purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection c, purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection c

radiography instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001085

An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects.
Source
http://en.wikipedia.org/wiki/Medical_radiography
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

radiolabel rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000163

a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection
has super-classes
molecular label role c
realized in op only radioactivity detection c

random access memoryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001877

Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location
Source
http://en.wikipedia.org/wiki/RAM last accessed: 2013-12-02
has super-classes
material information bearer c

random access memory sizec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001874

random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation
Source
PRS, AGB
Example
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads"
has super-classes
scalar measurement datum c
is about op some random access memory c and (part of op some computer c)

random primed DNA labelingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000879

a labeling in which random primers are used to uniformly label input DNA
Source
PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13.
Example
PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9.
has super-classes
addition of molecular label c

randomized complete block designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500007

A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
Source
http://www.tufts.edu/~gdallal/ranblock.htm
Example
http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
has super-classes
intervention design c
has sub-classes
graeco latin square design c, hyper graeco latin square design c, latin square design c

randomized group participant rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302846

a role that borne by an organism and realized by some group randomization process
Example
A person enrolled in a randomized clinical trial bears a randomized group participant role
is equivalent to
is_specified_output_of op some group randomization c
has super-classes
role c

rapid amplification of cDNA endsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002090

A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA.
Source
http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/RACE_Rapid_Amplification_of_cDNA_Ends/5_Prime_RACE_and_3_Prime_RACE
has super-classes
reverse transcribed polymerase chain reaction c
has sub-classes
3' rapid amplification of cDNA ends c, 5' rapid amplification of cDNA ends c

rapid resolution columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000493

A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102
has super-classes
material separation device c
has function op some material separation function c

rare earth metal atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33321

has super-classes
atom c

rate measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001554

A scalar measurement datum that represents the number of events occuring over a time interval
Source
IEDB
Example
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
has super-classes
scalar measurement datum c
has sub-classes
binding off rate measurement datum (koff) c, binding on rate measurement datum (kon) c

rate unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000280

A unit which represents a standard measurement occurrence of a process per unit time.
has super-classes
measurement unit label c
has members
count per molar ni, count per molar second ni, count per nanomolar ni, count per nanomolar second ni

ratio of collected to emitted lightc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000054

A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
Source
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
Example
10%
has super-classes
measurement datum c

Rattus norvegicusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10116

has super-classes
Murinae c

reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001879

A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
(copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
Source
PERSON:Matthew Brush
is equivalent to
material entity c and (has role op some reagent role c)
has super-classes
processed material c
is_specified_output_of op some material processing c
has sub-classes
forward PCR primer c, reverse PCR primer c

reagent application functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000960

A function that is realized when a reagent is automatically added to some research material.
Source
PERSON: Nicole Vasilevsky, Matthew Brush
Example
An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
has super-classes
function c
has sub-classes
addition of molecular tracer function c

reagent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000086

A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
Source
PERSON:Matthew Brush
Example
Buffer, dye, a catalyst, a solvating agent.
has super-classes
role c

real time polymerase chain reaction assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000893

A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
Source
WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
has super-classes
assay c
has part op some polymerase chain reaction c

real time reverse-transcription polymerase chain reaction assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000911

Is_a PCR real time preceded by a reverse transcription step (reverse transcription step = an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase)
is equivalent to
assay c and (has part op some real time polymerase chain reaction assay c and (immediately preceded by op some artificially induced reverse transcription c)) and (immediately preceded by op some artificially induced reverse transcription c)
has super-classes
assay c
has_specified_output op some information content entity c and (is about op some gene expression c)

real-time PCR machinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001110

An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
Source
http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
has super-classes
PCR instrument c

realizable entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000017

A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
has super-classes
specifically dependent continuant c
has sub-classes
disposition c, plan c, role c
is in domain of
realized in op
is in range of
realizes op
is disjoint with
quality c

recombinant BAC cloningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000790

Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material
Source
http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome
has super-classes
recombinant vector cloning c

recombinant phage cloningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000799

Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro.
Source
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611
Example
Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
has super-classes
recombinant vector cloning c

recombinant plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000410

a plasmid in which extraneous DNA has been inserted.
Source
GROUP: OBI Biomaterial Branch
is equivalent to
plasmid c and (is_specified_output_of op some recombinant vector cloning c)
has super-classes
plasmid c
recombinant vector c

recombinant plasmid cloningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600042

the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial
Source
OBI branch derived
Example
The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35.
is equivalent to
recombinant vector cloning c and (has_specified_input op some plasmid c and (has role op some cloning vector role c)) and (has_specified_output op some recombinant plasmid c)
has super-classes
recombinant vector cloning c

recombinant vectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000731

A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
is equivalent to
material entity c and (is_specified_output_of op some recombinant vector cloning c)
has super-classes
processed material c
has sub-classes
cDNA library c, phage display library c, recombinant plasmid c

recombinant vector cloningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600064

a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
Source
OBI branch derived
has super-classes
material processing c
realizes op some cloning vector role c
has_specified_input op some cloning vector c
has_specified_input op some material entity c and (has role op some cloning insert role c)
has_specified_output op some recombinant vector c
achieves_planned_objective op some material transformation objective c
has sub-classes
nucleotide overhang cloning c, recombinant BAC cloning c, recombinant YAC cloning c, recombinant phage cloning c, recombinant plasmid cloning c, recombination enzyme based cloning c, restriction enzyme based cloning c, vector mediated amplification c, vector mediated expression c

recombinant YAC cloningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000824

Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material
Source
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611
Example
Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
has super-classes
recombinant vector cloning c

recombination enzyme based cloningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000692

a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector
has super-classes
recombinant vector cloning c

record functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000368

A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation
has super-classes
function c

record of missing knowledgec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000852

a information content entity created to indicate that information about something is not available to the person recording it.
Source
Example
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
has super-classes
information content entity c
has sub-classes
record of unknown sex c

record of unknown sexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000858

a record indicating that the biological sex of an organism is not known.
Example
A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
has super-classes
record of missing knowledge c
is about op some biological sex c

reduced dimension data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000676

A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set.
is equivalent to
is_specified_output_of op some data vector reduction data transformation c
has super-classes
data set c

reduced representation bisulfite sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001862

A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol that enriches CG-rich parts of the genome.
Source
Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174]
Example
Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174]
has super-classes
bisulfite sequencing c
has part op some library preparation c
has part op some specific enzymatic cleavage c

reference designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500010

A reference experiment design type is where all samples are compared to a common reference.
Source
MO_699
Example
PMID: 12933549
has super-classes
study design c

reference subject rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000220

a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
Source
OBI
Example
Saline treated rat; one of three identically-treated subjects
has super-classes
participant under investigation role c
inheres in op some organism c or specimen c
has sub-classes
baseline participant role c, biological replicate role c, crossover population role c, technical replicate role c

reference substance rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000025

a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
Source
OBI
Example
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
has super-classes
role c
inheres in op some material entity c
has sub-classes
calibration substance role c, dye swap quality control role c, negative reference substance role c, nucleic acid template role c, positive reference substance role c, spike-in quality control role c

references sectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000320

A part of a document that has citations as parts
Example
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
has super-classes
document part c
has part op some citation c

Reflectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400089

A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells.
Source
http://www.i-cyt.com/reflection.htm
Example
Reflection at TSRI Flow Cytometry Core Facility
has super-classes
flow cytometer sorter c

refractive index detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000583

For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector.
Source
WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081
has super-classes
measurement device c
has function op some measure function c

regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000001

A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
has super-classes
generically dependent continuant c
has sub-classes
assembly c, miRNA c, polypeptide c, primary structure of DNA macromolecule c, primary structure of RNA molecule c

regression analysis methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200102

Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
Source
BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
has super-classes
data transformation c
has sub-classes
multiple linear regression analysis c, partial least square regression analysis c, principal component regression c

regulation of DNA methylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0044030

Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
has super-classes
regulation of molecular function, epigenetic c

regulation of gene expression, epigeneticc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0040029

Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.
has super-classes
regulation of molecular function, epigenetic c

regulation of molecular function, epigeneticc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0040030

Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya.
has super-classes
biological_process c
has sub-classes
regulation of DNA methylation c, regulation of gene expression, epigenetic c

regulation-assigned rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000016

Regulation-assigned role is a regulatory role defined by legislation or governmental orders
Example
Approval letter
has super-classes
regulatory role c
has sub-classes
role of certified IRB professional c, role of impartial witness c, role of legally acceptable representative c

regulator rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000014

a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Source
OBI
Example
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
has super-classes
regulatory role c
has sub-classes
role of Institutional Review Board c, role of regulator of chemical manufacturer c, role of regulator of consumables and medical devices c

regulatory agencyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000450

A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
Source
WEB: en.wikipedia.org/wiki/Regulator
Example
The US Environmental Protection Agency
is equivalent to
organization c and (has role op some regulator role c)
has super-classes
organization c

regulatory rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000017

a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
Source
OBI, CDISC
Example
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
has super-classes
role c
has sub-classes
regulation-assigned role c, regulator role c

relational qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000145

b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
a marriage bond, an instance of love, an obligation between one person and another.
has super-classes
quality c

relational spatial qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001631

A quality of related physical entities inhering in a bearer by virtue of the bearer's pertaining to or involving or having the nature of space in relation to another entity.
has super-classes
quality of related physical entities c
has sub-classes
anterior to c, dorsal to c, lateral to c, left side of c, right side of c, ventral to c

renal medullac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000362

the inner portion of the kidney consisting of the renal pyramids
has super-classes
multi-tissue structure c

renal medulla specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002521

A specimen that is derived from renal medulla.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some renal medulla c))
has super-classes
specimen from organism c

repeated measure designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500002

a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
Source
http://www.holah.karoo.net/experimentaldesigns.htm
Example
PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
has super-classes
intervention design c
has sub-classes
cross over design c

replicate analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200057

A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc.
Source
PERSON: Helen Parkinson
PERSON:Elisabetta Manduchi
Example
Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c
has sub-classes
dye swap merge c

replicate designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500018

A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Source
MO_885
has super-classes
study design c

reportc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000088

a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
Source
GROUP: OBI
OBI_0000099
Example
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
has super-classes
document c
has sub-classes
direct submission to IEDB c, investigation results report c, journal article c

reporter cell line analyte detection bioassayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000904

An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant.
Source
IEDB
Example
CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant.
has super-classes
analyte assay c
(realizes op some reagent role c and (inheres in op some cell line c)) and (has_specified_input op some cell line c)
has part op some maintaining cell culture c

reporter gene assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002082

An assay in which expression of a reporter gene is detected that was inserted under the control of a regulatory sequence of interest.
Source
Paul D. Thomas, Yang Chai; FaceBase
has super-classes
assay c
has sub-classes
enhancer activity detection by reporter gene assay c

reporting party rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000068

a study personnel role played by a party who reports the outcome of a study component
Source
OBI
Example
The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
has super-classes
investigation agent role c
has sub-classes
sequence annotation reporting role c

research organizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000828

An organization formed with a goal to have its members conduct investigations
Example
The SALK institute is a research organization.
has super-classes
organization c

response to stimulusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0050896

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
has super-classes
biological_process c
has sub-classes
cellular response to DNA damage stimulus c, immune response c

responsible party rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000102

a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
Source
OBI
Example
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
has super-classes
investigation agent role c
has sub-classes
principal investigator role c, sponsor role c, trial monitor role c

restricting MHC rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110086

The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell.
Source
IEDB
has super-classes
role c

restriction enzymec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000732

an enzyme that has a specific target cleavage sites within nucleic acids
Example
The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
has super-classes
enzyme c
protein c
has function op some catalytic activity c

restriction enzyme based cloningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000738

restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector.
has super-classes
recombinant vector cloning c
has part op some enzymatic ligation c
realizes op some cloning vector role c and (role of op some nucleic acid restriction enzyme digest c)
realizes op some cloning insert role c and (role of op some nucleic acid restriction enzyme digest c)

results sectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000318

A part of a publication about an investigation that is about a study design execution
Example
The section labelled 'results' in a typical scientific journal article
has super-classes
document part c
is about op some study design execution c

reverse PCR primerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001951

A short oligonucleotide complementary to target DNA (5'->3' on minus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm.
Source
adapted from "http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p"
Example
5' end of luciferase, reverse primer (LucNrev CCTTATGCAGTTGCTCTCC)
has super-classes
deoxyribonucleic acid c
reagent c
deoxyribonucleic acid c and (has role op some reagent role c)
(has part op some deoxyribonucleic acid c) and (is_specified_input_of op some real time polymerase chain reaction assay c or real time reverse-transcription polymerase chain reaction assay c)

reverse transcribed polymerase chain reactionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000552

reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
Example
Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
has super-classes
enzymatic amplification c
has part op some polymerase chain reaction c and (immediately preceded by op some artificially induced reverse transcription c)
has_specified_input op some ribonucleic acid c
has_specified_output op some PCR product c
has sub-classes
rapid amplification of cDNA ends c

reverse transcriptasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000419

enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
Source
group:OBI
is equivalent to
enzyme c and (has function op some RNA-directed DNA polymerase activity c)
has super-classes
enzyme c

reverse transcription polymerase chain reaction assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001170

an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
Source
GROUP: Penn Group
has super-classes
assay c
has part op some reverse transcribed polymerase chain reaction c
has_specified_input op some ribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some information content entity c and (is about op some gene expression c)

reversed phase columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000510

A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106
has super-classes
chromatography column c

rhodium atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33359

A cobalt group element atom that has formula Rh.
has super-classes
molecular entity c

Rhodium DNA structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001018

a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhodium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:2843807
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some rhodium atom c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)
achieves_planned_objective op some assay objective c

RIA measuring binding of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001649

A B cell epitope qualitative binding to antibody assay that uses a radio immuno assay.
Source
IEDB
is equivalent to
assay measuring qualitiative binding of a B cell epitope:antibody complex c and (has part op some radio immuno assay c)
has super-classes
radioactivity detection binding assay c
assay measuring qualitiative binding of a B cell epitope:antibody complex c

RIA measuring the association constant [KA] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001736

A B cell epitope equilibrium association constant (KA) determination assay that uses a radio immuno assay.
Source
IEDB
is equivalent to
assay measuring the association constant [KA] of a B cell epitope:antibody complex c and (has part op some radio immuno assay c) and (has_specified_output op some has measurement unit label op value count per nanomolar)
has super-classes
radioactivity detection binding assay c
assay measuring the association constant [KA] of a B cell epitope:antibody complex c

RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001727

A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a radio immuno assay.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c and (has part op some radio immuno assay c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
radioactivity detection binding assay c
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c

ribonuclease CL3c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000025478

A protein with ribonuclease activity that is purified from chicken liver.
has super-classes
protein c

ribonuclease T2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000014060

A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof.
has super-classes
protein c

ribonuclease U2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000025475

A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof.
has super-classes
protein c

ribonuclease V1c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000025477

A protein with ribonuclease activity that is a constituent of cobra venom.
has super-classes
protein c

ribonucleic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33697

High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
has super-classes
nucleic acid c

ribosomal profiling by sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002038

A RNA-seq assay to sequence only mRNA protected by the ribosome during translation.
Source
Ingolia, Nicholas T. (28 January 2014). "Ribosome profiling: new views of translation, from single codons to genome scale". Nature Reviews Genetics 15 (3): 205-213. doi:10.1038/nrg3645. PMID 24468696.
Example
Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528
has super-classes
RNA-seq assay c

right cerebral hemispherec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002813

A cerebral hemisphere that is in the right side of a brain.
has super-classes
material anatomical entity c

right handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0002203

Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
has super-classes
handedness c

right side ofc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001793

A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity.
has super-classes
relational spatial quality c

RMA cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110038

A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface.
Source
IEDB
has super-classes
immortal cell line c

RNA ADA I RNA structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001019

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNA adenosine deaminase I as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:7527340
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c
realizes op some catalytic activity c and (inheres in op some double-stranded RNA-specific adenosine deaminase c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001864

An assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing.
Source
Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248]
Example
Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248]
has super-classes
transcription profiling assay c
sequencing assay c
has part op some library preparation c
has part op some RNA sequencing c
has part op some non specific enzymatic cleavage c
has_specified_input op some ribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some transcription start site identification objective c
has participant op some DNA sequencer c

RNA Bind-n-Seq assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002044

A RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs)
Source
Lambert et al., (June 2014). "RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins." Mol Cell. 2014 Jun 5;54(5):887-900. doi: 10.1016/j.molcel.2014.04.016
has super-classes
RNA-seq assay c

RNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000880

an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
Source
Group: UPenn Group
has super-classes
nucleic acid extract c
is_specified_output_of op some RNA extraction c
has grain op some ribonucleic acid c
has sub-classes
cytoplasmic RNA extract c, nuclear RNA extract c, organellar RNA extract c, polyA RNA extract c, total RNA extract c

RNA extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0666666

A RNA extraction is a nucleic acid extraction where the desired output material is RNA
Source
OBI branch derived
has super-classes
nucleic acid extraction c
has_specified_output op some ribonucleic acid c
has sub-classes
cytoplasmic RNA extraction c, nuclear RNA extraction c, organellar RNA extraction c, polyA RNA extraction c, total RNA extraction c, viral RNA extraction c

RNA extraction/purification instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001050

A device that is used to isolate and collect RNA for subsequent molecular analysis.
Source
PERSON: Erik Segerdell
has super-classes
nucleic acid extraction/purification instrument c

RNA protection assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001670

RPA is a technique to assess the presence and estimate abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest.
Source
adapted from wikipedia + PMID:16491611
Example
Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. Wildey GM, Billetz AC, Matyas JR, Adams ME, McDevitt CA. J Orthop Res. 2001 Jul;19(4):650-8. PMID: 11518275
has super-classes
assay c
(assay c and (has_specified_input op some RNA extract c) and (has_specified_output op some data item c and (is about op some gene expression c))) and (achieves_planned_objective op some assay objective c)

RNA sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001177

RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact
Source
Bjoern Peters
is equivalent to
(has_specified_input op some ribonucleic acid c and (has role op some evaluant role c)) and (has_specified_output op some information content entity c and (is about op some primary structure of RNA molecule c))
has super-classes
sequencing assay c

RNA stability designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001306

A study design that examines the stability and/or decay of RNA transcripts.
Source
MO_553 RNA_stability_design
has super-classes
study design c
has part op some molecular feature identification objective c and (is about op some ribonucleic acid c)

RNA-binding protein immunoprecipitation array profiling assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001918

An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs).
Source
Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495]
Example
Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495]
has super-classes
analyte assay c
has part op some immunoprecipitation c
has part op some library preparation c
realizes op some evaluant role c and (role of op some protein complex c)
has_specified_output op some measurement datum c
achieves_planned_objective op some analyte measurement objective c
achieves_planned_objective op some protein and RNA interaction identification objective c
has participant op some DNA microarray c
has sub-classes
RNA-binding protein immunoprecipitation tiling array profiling c

RNA-binding protein immunoprecipitation tiling array profilingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001921

A RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs).
Source
Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495]
Example
Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495]
has super-classes
RNA-binding protein immunoprecipitation array profiling assay c
has participant op some tiling microarray c

RNA-directed DNA polymerase activityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0003964

Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
has super-classes
catalytic activity c

RNA-seq assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001271

An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
Source
EFO_0002770 transcription profiling by high throughput sequencing
has super-classes
transcription profiling assay c
sequencing assay c
realizes op some analyte role c and (role of op some ribonucleic acid c)
has_specified_input op some specimen c and (has part op some ribonucleic acid c)
has_specified_output op some sequence data c and (is about op some gene expression c)
achieves_planned_objective op some transcription profiling identification objective c
has participant op some DNA sequencer c
has sub-classes
RNA Bind-n-Seq assay c, bromouridine labeling and sequencing c, bromouridine pulse-chase and sequencing c, microRNA profiling by high throughput sequencing assay c, poly(A)-site sequencing assay c, ribosomal profiling by sequencing assay c, self-transcribing active regulatory region sequencing assay c, small RNA-seq c, transcript leader sequencing c, translation-associated transcript leader sequencing c

RNAi profiling by array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001304

An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
Source
EFO_0001030 RNAi profiling by array
has super-classes
analyte assay c
realizes op some analyte role c and (role of op some ribonucleic acid c)
achieves_planned_objective op some molecular feature identification objective c
has participant op some DNA microarray c

RNAi profiling by array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001286

A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
Source
Group: ArrayExpress production team
has super-classes
study design c
has part op some molecular feature identification objective c
is concretized as op some realized in op some (has part op some RNAi profiling by array assay c) and (has participant op some DNA microarray c)

RNASE CL3 structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001005

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse CL3 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:16453415
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c
realizes op some catalytic activity c and (inheres in op some ribonuclease CL3 c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

RNASE T1 structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001030

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:114514
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c
realizes op some catalytic activity c and (inheres in op some guanyl-specific ribonuclease T1 c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

RNASE T2 structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001021

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:6207483
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c
realizes op some catalytic activity c and (inheres in op some ribonuclease T2 c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

RNASE U2 structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001024

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAase U2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:409999
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c
realizes op some catalytic activity c and (inheres in op some ribonuclease U2 c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

RNASE V1 structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001012

a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse V1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:7031604
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c
realizes op some catalytic activity c and (inheres in op some ribonuclease V1 c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001857

An assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs).
Source
Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659]
Example
Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659]
has super-classes
analyte assay c
sequencing assay c
has part op some immunoprecipitation c
has part op some library preparation c
has part op some cross linking c
has part op some RNA sequencing c
has_specified_input op some protein complex c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some analyte measurement objective c
achieves_planned_objective op some protein and RNA interaction identification objective c
has participant op some DNA sequencer c
has participant op some sonicator c

rockerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001103

A device that provides three-dimensional motion for biomedical applications (e.g., gel trays).
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some mechanical function c

rodent carec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000728

rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research.
Source
PPPB branch
Example
keeping animal
has super-classes
laboratory animal care c
has part op some animal feeding c
realizes op some contain function c and (inheres in op some animal cage c)
realizes op some concretizes op some rodent care protocol c
has_specified_input op some Rodentia c
has_specified_output op some Rodentia c

rodent care protocolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000688

A rodent care protocol is an animal protocol in which the animals being taken care of are rodents.
Source
Bjoern Peters
Example
Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
has super-classes
animal care protocol c

Rodentiac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_9989

has super-classes
Euarchontoglires c
has sub-classes
Murinae c

rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000023

A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
has super-classes
realizable entity c
has sub-classes
accessed material role c, adjuvant role c, analyte role c, antigen role c, assay antigen role c, author role c, buffer role c, centrifuge pellet role c, cloning insert role c, complementary nucleotide probe role c, contact representative role c, detector reagent role c, donor c, drug role c, evaluant role c, host of immune response role c, host role c, immune epitope carrier role c, immunogen role c, investigation agent role c, manufacturer role c, material to be added role c, molecular label role c, nutrient role c, participant under investigation role c, pathogen role c, patient role c, randomized group participant role c, reagent role c, reference substance role c, regulatory role c, restricting MHC role c, service consumer role c, service provider role c, solute role c, solvent role c, specimen role c, study group role c, supernatant role c, target of material addition role c, test substance role c
is in range of
has role op
is disjoint with
disposition c

role of being consumer safety officerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000006

the role of a human being that is realized by enforcing regulations to ensure consumer safety
Source
OBI, CDISC
Example
Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
Person charged with serving as CSO, FDA official who coordinates the review
has super-classes
role of regulator of consumables and medical devices c

role of certified IRB professionalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000092

a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA
Source
WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional
Example
CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
has super-classes
regulation-assigned role c

role of impartial witnessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000196

a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial
Example
According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
has super-classes
regulation-assigned role c

role of independent data monitoring committeec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000144

a trial monitor role charged recommending whether to continue, modify, or end the trial
has super-classes
trial monitor role c

role of Institutional Review Boardc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000154

the role of a organization that is realized by members reviewing study designs for their agreement with regulations
Source
OBI, CDISC
Example
An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008
Animal protocol review board
has super-classes
regulator role c

role of legally acceptable representativec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000215

a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial.
Source
OBI, CDISC
Example
Parent of minor patient; Definition of legally acceptable representative An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE
has super-classes
regulation-assigned role c

role of pathology review boardc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000188

a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
has super-classes
worker role c

role of regulator of chemical manufacturerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000089

a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
Source
OBI
Example
EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm
has super-classes
regulator role c

role of regulator of consumables and medical devicesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000273

a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices
Source
OBI, CDISC
Example
FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html
has super-classes
regulator role c
has sub-classes
notified body role c, role of being consumer safety officer c

row submatrix extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200075

A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
Example
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set.
has super-classes
submatrix extraction c

rulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000055

a rule is an executable which guides, defines, restricts actions
Source
OBI_0500021
PRS
Example
example to be added
has super-classes
conditional specification c
has sub-classes
compliance rule c, stopping rule c

running titlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000329

A shorter version of a document title
has super-classes
document title c

ruthenium atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_30682

An iron group element atom that has formula Ru.
has super-classes
molecular entity c

Ruthenium structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001038

is a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhutenium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNAOntology
Example
PMID:3016894
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some ruthenium atom c)
has_specified_input op some deoxyribonucleic acid c or ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

s transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200110

An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization.
Source
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Example
This type of transformation is typically used in flow cytometry.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

s v n repositoryc back to ToC or Class ToC

IRI: http://usefulinc.com/ns/doap#SVNRepository

is defined by
http://usefulinc.com/ns/doap
has super-classes
thing c
has members
repository ni, repository ni

Saccharomyces cerevisiaec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_4932

has super-classes
saccharomyceta c

saccharomycetac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_716545

has super-classes
Ascomycota c
has sub-classes
Neurospora c, Saccharomyces cerevisiae c

SAGE ditag library preparationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002028

A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library.
Source
PMID:15905473
has super-classes
library preparation c

salivac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001836

A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
has super-classes
organism substance c

saliva specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002507

A specimen that is derived from saliva.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some saliva c))
has super-classes
specimen from organism c

sample from organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000671

a material obtained from an organism in order to be a representative of the whole
is equivalent to
(is_specified_output_of op some collecting specimen from organism c) and (has role op some material sample role c)
has super-classes
material sample c
specimen from organism c
derives from op some material anatomical entity c

sample injection systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000504

An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057
has super-classes
chromatography device c
has sub-classes
auto injector c, manual injection system c, splitless GC injector c

sample inletc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000497

The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head.
Source
WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044
has super-classes
chromatography device c

sample preparation for assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000073

A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
Source
OBI branch derived
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c
has sub-classes
sample preparation for sequencing assay c

sample preparation for sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001902

A sample preparation for assay that preparation of nucleic acids for a sequencing assay
Source
NIAID GSCID-BRC metadata working group
is equivalent to
sample preparation for assay c and (has_specified_input op some specimen c and (has grain op some nucleic acid c)) and (has_specified_output op some specimen c and (is_specified_input_of op some sequencing assay c))
has super-classes
sample preparation for assay c

sampling time measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001508

A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
Source
MO_738 timepoint
has super-classes
time measurement datum c

scaffold N50c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001945

N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information
Source
adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
Example
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
has super-classes
N50 c
is about op some supercontig c and (is_specified_output_of op some sequence assembly process c)

scalar measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000032

a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
Example
10 feet. 3 ml.
has super-classes
measurement datum c
has value specification op some scalar value specification c
has measurement unit label op min 1
has measurement value dp min 1
has sub-classes
N50 c, half maximal effective concentration (EC50) c, half maximal inhibitory concentration (IC50) c, length measurement datum c, mass measurement datum c, minimal inhibitory concentration c, random access memory size c, rate measurement datum c, scalar score from composite inputs c, time measurement datum c
is in domain of
has measurement value dp

scalar score from composite inputsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000970

A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
Source
Person: Jessica Turner
has super-classes
scalar measurement datum c
is_specified_output_of op some data transformation c
has measurement value dp min 1
has sub-classes
Edinburgh score c

scalar value specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001931

A value specification that consists of two parts: a numeral and a unit label
has super-classes
value specification c
has measurement unit label op min 1
has specified value dp min 1
has sub-classes
mass value specification c

scaling data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200185

A scaling data transformation is a data transformation that has objective scaling.
Source
PERSON: James Malone
is equivalent to
achieves_planned_objective op some scaling objective c
has super-classes
data transformation c
has sub-classes
loess scale group transformation c

scaling objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200183

is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum
Example
Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13
has super-classes
data transformation objective c

scanning force microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001105

A microscope that forms images of surfaces using a physical probe that scans the specimen.
Source
http://en.wikipedia.org/wiki/Scanning_probe_microscopy
has super-classes
microscope c
has function op some measure function c

scatter plotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000184

A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
Source
WEB: http://en.wikipedia.org/wiki/Scatterplot
Example
Comparison of gene expression values in two samples can be displayed in a scatter plot
has super-classes
graph c

scattered molecular aggregatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000576

a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
Source
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
Example
the sodium and chloride ions in a glass of salt water
has super-classes
material entity c
has grain op some molecular entity c
has grain op only molecular entity c
has sub-classes
dissolved material entity c

Schizosaccharomyces pombec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_4896

has super-classes
Ascomycota c

scintillation counterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001070

A device that is used to measure ionizing radiation.
Source
http://en.wikipedia.org/wiki/Scintillation_counter
has super-classes
measurement device c
has function op some measure function c

screening libraryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100064

a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?
Source
GROUP: IEDB
Example
PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
has super-classes
processed material c

secondary cultured cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001866

A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
Source
PERSON: Matthew Brush
has super-classes
cultured cell c
(is_specified_output_of op some cell culture splitting c) or (derives from op some is_specified_output_of op some cell culture splitting c)
derives from op some primary cultured cell c
has sub-classes
cell line cell c

secondary cultured cell populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001905

A cultured cell population that is derived through one or more passages in culture.
The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.
Source
PERSON:Matthew Brush
has super-classes
cultured cell population c
is_specified_output_of op some cell culture splitting c
has grain op some secondary cultured cell c
has grain op only secondary cultured cell c
has sub-classes
cell line c

secondary structure of RNA moleculec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000896

Example
PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
has super-classes
secondary structure of sequence macromolecule c

secondary structure of sequence macromoleculec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000885

A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford.
Source
Wikipedia
has super-classes
quality of a single physical entity c
has sub-classes
secondary structure of RNA molecule c

selectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001928

A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
Source
OBI
Example
PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
is equivalent to
realizes op some concretizes op some selection criterion c
has super-classes
planned process c
has sub-classes
acquisition c, human subject enrollment c

selection by survivalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600054

the use of environmental conditions to select for the organism or cells that have a certain trait
Source
OBI branch derived
Example
The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

selection criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001755

A directive information entity which defines and states a principle of standard by which selection process may take place.
Source
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
Example
rats should be aged between 6 and 8 weeks and weight between 180-250grams
has super-classes
directive information entity c
has sub-classes
eligibility criterion c

selective organism creation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001175

an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
Source
WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29
has super-classes
objective specification c

selectively maintained organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001185

An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
Source
MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
is equivalent to
organism c and (is_specified_output_of op some planned process c and (achieves_planned_objective op some selective organism creation objective c))
has super-classes
organism c

self reported handedness assessmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000957

An assay in which a person makes a statement that indicates what handedness he has from a choice of different categories.
has super-classes
handedness assay c
has_specified_output op some categorical measurement datum c and (is quality measurement of op some handedness c)

self vs self designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500019

A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared.
Source
MO_490
Example
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
has super-classes
study design c

self-organizing mapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000701

A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these.
Source
PERSON: Ryan Brinkman
has super-classes
class discovery data transformation c
(has_specified_output op some clustered data set c or topologically preserved clustered data set c) and (achieves_planned_objective op some class discovery objective c)

self-transcribing active regulatory region sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002041

A RNA-seq assay to identify the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA.
Source
Arnold et al. (January 2013). "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq". Science 339 (6123): 1074-7.
Example
Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765.
has super-classes
RNA-seq assay c

separation into different composition objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000681

A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
Example
The objective to obtain cells contained in a sample of blood.
has super-classes
material separation objective c
has sub-classes
purification objective c
is disjoint with
portioning objective c

sequence analysis data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200187

A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns.
Source
EDITOR
is equivalent to
achieves_planned_objective op some sequence analysis objective c
has super-classes
data transformation c
has sub-classes
b cell epitope prediction c, mhc binding prediction c, sequence library deconvolution c, t cell epitope prediction c

sequence analysis objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200081

A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
Source
PERSON: James Malone
has super-classes
data transformation objective c

sequence annotationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001944

A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data.
Source
NIAID GSCID-BRC metadata working group
has super-classes
planned process c
realizes op some concretizes op some sequence annotation algorithm c
has_specified_input op some sequence data c
has_specified_output op some sequence feature annotation c

sequence annotation algorithmc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001625

An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation.
Source
NIAID GSCID-BRC metadata working group
has super-classes
algorithm c

sequence annotation providerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001947

A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence.
Source
NIAID GSCID-BRC metadata working group
is equivalent to
(Homo sapiens c or organization c) and (has role op some sequence annotation reporting role c)
has super-classes
material entity c

sequence annotation reporting rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001949

A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence.
Source
NIAID GSCID-BRC metadata working group
has super-classes
reporting party role c

sequence assembly algorithmc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001522

An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
Source
NIAID GSCID-BRC metadata working group
has super-classes
algorithm c

sequence assembly namec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001948

A textual entity that is used to denote a sequence assembly.
Source
NIAID GSCID-BRC metadata working group
is equivalent to
textual entity c and (denotes op only sequence_assembly c)
has super-classes
textual entity c

sequence assembly processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001872

A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs).
Source
NIAID GSCID-BRC metadata working group
has super-classes
data transformation c
realizes op some concretizes op some sequence assembly algorithm c
has_specified_input op some sequence data c
has_specified_output op some sequence data c
has_specified_output op some genome coverage c
has_specified_output op some N50 c

sequence datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000973

A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
Source
GROUP: OBI
Example
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
has super-classes
measurement datum c
measurement datum c and (is about op some region c)
has sub-classes
DNA sequence data c

sequence feature annotationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000905

Information about a sequence region
place holder for sequence ontology term
Source
Bjoern Peters
has super-classes
information content entity c
has sub-classes
transcription factor binding site c

sequence feature identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000113

Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
has super-classes
biological feature identification objective c
has sub-classes
protein and DNA interaction identification objective c, protein and RNA interaction identification objective c

sequence library deconvolutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001966

is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to pull together all reads belonging to a given single sample following the sequencing of a multiplexed library which combining several samples in one sequencing event
Source
PRS for OBI
has super-classes
sequence analysis data transformation c
preceded by op some DNA sequencing c and (has_specified_input op some multiplexed sequencing library c)
achieves_planned_objective op some sequence analysis objective c

sequence-specific DNA bindingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0043565

Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
has super-classes
binding c

sequence_assemblyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000353

A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
has super-classes
assembly c
has sub-classes
contig c, supercontig c

sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600047

the use of a chemical or biochemical means to infer the sequence of a biomaterial
Source
OBI branch derived
Example
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
is equivalent to
(has_specified_output op some sequence data c) and (achieves_planned_objective op some assay objective c)
has super-classes
assay c
has_specified_input op some (deoxyribonucleic acid c or ribonucleic acid c or protein c) and (has role op some evaluant role c)
has sub-classes
Carbon-copy chromosome conformation capture assay c, ChIP-seq assay c, DNA replication timing by sequencing assay c, DNA sequencing c, Edman degradation c, MeDIP-seq assay c, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay c, RNA sequencing c, RNA-seq assay c, RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay c, cap analysis of gene expression c, chromatin interaction analysis by paired-end tag sequencing c, cross-linking immunoprecipitation high-throughput sequencing assay c, micrococcal nuclease digestion followed by high throughput sequencing assay c, protein sequencing by tandem mass spectrometry assay c, taxonomic diversity assessment by targeted gene survey c, transcript analysis by paired-end tag sequencing c

sequencing facility contact personc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001888

A person who is the contact representative at the sequencing facility
Source
NIAID GSCID-BRC metadata working group
is equivalent to
Homo sapiens c and (is member of organization op some sequencing facility organization c) and (has role op some contact representative role c)
has super-classes
Homo sapiens c

sequencing facility organizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001891

An organization that provides sequence determination service
Source
NIAID GSCID-BRC metadata working group
is equivalent to
organization c and (has role op some service provider role c and (realized in op some sequencing service c))
has super-classes
organization c

sequencing library multiplexingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001959

a planned process which consists in running a set of samples as a pool in one single instrument run of data acquisition process while retaining the ability to associate individual results to each of the individual input samples thanks to the use of a multiplex identifier, introduced during the ligation step of the individual library preparation and specific to a given sample.
Source
OBI
Example
http://www.illumina.com/technology/multiplexing_sequencing_assay.ilmn
has super-classes
material processing c

sequencing servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001904

A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
Source
Adpated from 'DNA sequencing service'
is equivalent to
material service c and (provides_service_consumer_with op some sequencing assay c)
has super-classes
material analysis service c
has sub-classes
DNA sequencing service c

sequential designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0300310

Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does
Source
MUSC
Example
PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs.
has super-classes
intervention design c

serial analysis of gene expressionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002029

A transcription profiling assay which aims to quantify RNA through creating short signature tags of the messages and ligating them into a larger molecule that is than sequenced.
Source
PMID:7570003
Example
PMID:15905473
has super-classes
transcription profiling assay c
has part op some SAGE ditag library preparation c
has part op some sequencing assay c
has participant op some DNA sequencer c

serial numberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000131

A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
has super-classes
symbol c

serum neutralization of viral infectivity assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000872

A quantitative assay where different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect. The simple process of dilution provides a way to compare the virus- neutralizing abilities of different sera. The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked.
Source
WEB: http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/
has super-classes
analyte assay c
achieves_planned_objective op some analyte measurement objective c
has sub-classes
96-well neutralization assay c

servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001173

A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
Source
OBI workshop San Diego 2011
Example
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
is equivalent to
planned process c and ((realizes op some service consumer role c) and (realizes op some service provider role c))
has super-classes
planned process c
has part op some planned process c
has sub-classes
access service c, data service c, material service c, support service c, training service c
is in domain of
provides_service_consumer_with op

service consumer rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000941

a role which inheres in a person who uses a service
Source
OBI
Example
A biologist who uses a sequencing services fulfills the role of a service consumer
has super-classes
role c
inheres in op some Homo sapiens c or organization c

service provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000947

is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
Example
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
has super-classes
role c
inheres in op some Homo sapiens c or organization c
realized in op only planned process c
has sub-classes
material supplier role c

service provision objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000993

An objective which is fulfilled by the provision of some service e.g. a training service
Source
OBI
Example
A sequencing centre has a service provision objective
has super-classes
objective specification c

setting datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000140

A settings datum is a datum that denotes some configuration of an instrument.
has super-classes
data item c

sex comparison designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001426

A study design that assays differences associated with an organism's sex, gender or mating type.
Source
MO_575 sex_design
has super-classes
study design c
has part op some organism feature identification objective c
has part op some study design independent variable c and (is about op some biological sex c)

sheath tankc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400094

Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
LSR2 sheath tank
has super-classes
physical store c
has function op some contain function c
has function op some environment control function c

short pass filterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400095

A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm.
Source
http://en.wikipedia.org/wiki/Low-pass_filter
Example
620 SP filter
has super-classes
optical filter c

shotgun bisulfite-seq assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001863

A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing.
Source
Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]
Example
Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030].
has super-classes
bisulfite sequencing c
has part op some library preparation c
has participant op some sonicator c

signal amplification functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000395

A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal.
has super-classes
signal conversion function c

signal conversion functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000393

A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon.
has super-classes
information processor function c
has sub-classes
signal amplification function c

similarity calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200113

A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are.
Source
PERSON: Elisabetta Manduchi
has super-classes
class prediction data transformation c
class discovery data transformation c
has_specified_output op some classified data set c
has_specified_output op some clustered data set c
has sub-classes
euclidean distance calculation c, pearson correlation coefficient calculation c

sine transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200016

A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html.
Source
WEB: http://mathworld.wolfram.com/Sine.html
Example
sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

single blind study executionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000822

A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated
Source
http://clinicaltrials.gov/ct2/info/glossary#single
is equivalent to
treatment portion of study execution c and (has part op only not (informing subject of study arm c))
has super-classes
treatment portion of study execution c
has sub-classes
double blind study execution c

single fragment libraryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000736

is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
has super-classes
processed material c

single linkage hierarchical clusteringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200045

A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster.
Source
PERSON: Elisabetta Manduchi
has super-classes
agglomerative hierarchical clustering c

single-nucleotide-resolution nucleic acid structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000870

is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity.
Source
RNAO
Example
is equivalent to
(has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c)) and (achieves_planned_objective op some assay objective c)
has super-classes
assay c
has sub-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c, single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing c

single-nucleotide-resolution nucleic acid structure mapping assay using chemical probingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001017

a single-nucleotide-resolution nucleic acid structure mapping assay which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
Source
RNAO and OBI
is equivalent to
(realizes op some reagent role c and (inheres in op some molecular entity c or nucleic acid c)) and (has_specified_output op some measurement datum c and (is about op some secondary structure of sequence macromolecule c))
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay c
has sub-classes
CMCT structure mapping assay c, DEPC structure mapping assay c, DMS structure mapping assay c, ENU structure mapping assay c, Fe-BABE RNA structure mapping assay c, Lead structure mapping assay c, MPE-Fe(II) structure mapping assay c, NMIA RNA structure mapping assay c, OH-radical structure mapping assay c, Rhodium DNA structure mapping assay c, Ruthenium structure mapping assay c, Terbium RNA structure mapping assay c, inline probing RNA structure mapping c, kethoxal structure mapping assay c

single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001014

a single-nucleotide-resolution nucleic acid structure mapping assay which relies on proteins acting as enzymatic probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
Source
RNAO and OBI
is equivalent to
realizes op some catalytic activity c and (inheres in op some protein c)
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay c
has sub-classes
DNASE 1 structure mapping assay c, Nuclease S1 structure mapping assay c, RNA ADA I RNA structure mapping assay c, RNASE CL3 structure mapping assay c, RNASE T1 structure mapping assay c, RNASE T2 structure mapping assay c, RNASE U2 structure mapping assay c, RNASE V1 structure mapping assay c, parallel analysis of RNA structure c

sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000029

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
has super-classes
immaterial entity c
has sub-classes
geographic location c, interrogation_point c, jet_in_air_flow_chamber c
is disjoint with
spatial region c, continuant fiat boundary c

size exclusion columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000618

A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100
has super-classes
chromatography column c
has sub-classes
gel filtration column c

skeletal muscle tissuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001134

Muscle tissue that consists primarily of skeletal muscle fibers.
has super-classes
tissue c

skeletal muscle tissue specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002519

A specimen that is derived from skeletal muscle.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some skeletal muscle tissue c))
has super-classes
specimen from organism c

skewness calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200123

A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment
Source
WEB: http://www.riskglossary.com/link/skewness.htm
has super-classes
center calculation data transformation c
descriptive statistical calculation data transformation c
(has_specified_output op some center value c) and (achieves_planned_objective op some center calculation objective c)
achieves_planned_objective op some descriptive statistical calculation objective c

skin of bodyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002097

The organ covering the body that consists of the dermis and epidermis.
has super-classes
material anatomical entity c

skin of body specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002526

A specimen that is derived from skin.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some skin of body c))
has super-classes
specimen from organism c

slide warmerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001131

A device that is used to heat microscope slides.
Source
PERSON: Erik Segerdell
has super-classes
environmental control device c
has function op some heat function c

small RNA-seqc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002112

An RNA-seq assay which is targeting small RNA (17-35 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits.
Source
http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html
has super-classes
RNA-seq assay c

small-angle scattering assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002108

A 3D structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined.
Source
IEDB
Example
Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein
has super-classes
3D structure determination assay c

small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002101

A B cell epitope 3D structure determination assay that uses a small-angle scattering assay.
Source
IEDB
is equivalent to
3D structure determining assay of a 3D B cell epitope:antibody complex c and (has part op some small-angle scattering assay c)
has super-classes
3D structure determining assay of a 3D B cell epitope:antibody complex c

small-animal image acquisition devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001077

A device that is used to image small laboratory animals (e.g., rats and mice) in vivo.
Source
PERSON: Erik Segerdell
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

SNP microarrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001204

a DNA microarray used to detect polymorphisms in DNA samples
Source
EFO_0002703 SNP array
has super-classes
DNA microarray c

sodium chloridec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_26710

An inorganic chloride salt having sodium(1+) as the counterion.
has super-classes
molecular entity c

sodium citrate dihydratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_32142

The dihydrate of trisodium citrate.
has super-classes
molecular entity c

sodium phosphatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_37586

has super-classes
molecular entity c

soft independent modeling of class analogy analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200098

Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes.
Source
WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

softwarec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000010

Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
Source
GROUP: OBI
has super-classes
plan specification c
has sub-classes
GenePattern software c, software application c, software library c, software method c, software module c, software script c

software applicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000594

A software application is software that can be directly executed by some processing unit.
Source
http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
has super-classes
software c

software interpreterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000065

A software interpreter is a software application that executes some specified input software.
Source
OBI_0000199
group:OBI
Example
R program, Perl interpreter, Java virtual machine
has super-classes
algorithm c

software libraryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000593

A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
Source
http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
has super-classes
software c

software methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000591

A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
Source
http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
has super-classes
software c

software modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000592

A software module is software composed of a collection of software methods.
Source
http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
has super-classes
software c

software optimization objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000055

Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
has super-classes
software testing objective c

software pipelinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001943

A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements.
Source
WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29
has super-classes
plan specification c

software scriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000595

A software script is software whose instructions can be executed using a software interpreter.
Source
http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
has super-classes
software c

software testing objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000242

Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
has super-classes
methodology testing objective c
has sub-classes
software optimization objective c

soilc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_00001998

Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.
has super-classes
material entity c
has sub-classes
podzol c

Solexa sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000724

is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing.
Source
adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
Example
PMID: 18987734 Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9.
has super-classes
DNA sequencing by synthesis c
has_specified_input op some paired-end library c or single fragment library c
has participant op some Illumina Genome Analyzer II c
immediately preceded by op some immobilization c and (immediately preceded by op some vector mediated amplification c)

SOLiD 3 Plus Systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002007

A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
Source
http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf
Example
Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407
has super-classes
AB SOLiD System c
is_manufactured_by op value Applied Biosystems

SOLiD 4 Systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002024

An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
Source
http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4
has super-classes
AB SOLiD System c
is_manufactured_by op value Applied Biosystems

solid NMR probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000479

An NMR probe that is designed to hold a solid sample.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243
has super-classes
NMR probe c
has sub-classes
tecmag EAGLE probe c

SOLiD sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000706

is a DNA sequencing which allows sequence identification by relying on the following steps: 1. Primers hybridize to the P1 adapter sequence within the library template. 2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. 3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. 4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles
Source
adapted from Wikipedia and Applied Biosystems web site
Example
PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
has super-classes
DNA sequencing by ligation c
has_specified_input op some DNA ligase c
has_specified_input op some paired-end library c or single fragment library c
has participant op some AB SOLiD System c
immediately preceded by op some immobilization c and (immediately preceded by op some vector mediated amplification c)

solid state laserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400096

A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser.
Source
http://en.wikipedia.org/wiki/Solid-state_laser
Example
Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command
has super-classes
laser c
has sub-classes
neodymium-YAG laser c

solid support functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000399

A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
Example
Taped, glued, pinned, dried or molecularly bonded to a solid support
has super-classes
function c

solute rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302733

solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
Source
adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)
Example
PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure.
has super-classes
role c
inheres in op some molecular entity c
realized in op only creating a mixture of molecules in solution c

solvent mixerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000469

A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072
has super-classes
chromatography instrument c

solvent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302732

solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation
Source
adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)
Example
PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors.
has super-classes
role c
inheres in op some molecular entity c
realized in op only creating a mixture of molecules in solution c

Somacountc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400097

A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk.
Source
http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575
has super-classes
flow cytometer analyzer c

SomaScopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400098

The SomaScope is an instrument to quantify somatic cells in milk.
Source
"http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10"
Example
SomaScope Mark II Automatic Economical
has super-classes
flow cytometer analyzer c

sonicatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400114

A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions.
Source
MO
Example
Sonicator 3000
has super-classes
perturbation device c
has function op some perturb function c

sort functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000403

A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
has super-classes
material separation function c

Sos-recruitment assay c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001680

is a kind of yeast 2 hybrid system where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature. Using the Sos recruitment system, interacting proteins for targeted domain can be detected.
Source
adapted from the original publication by Aronheim et al, 1997. PMID: 9154808
Example
The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. Schönhofer-Merl S, Torres-Ruiz RA. Mol Genet Genomics. 2010 May;283(5):439-49. Epub 2010 Mar 19. PMID: 20300944
has super-classes
binding assay c
(assay c and (has_specified_input op some genetically modified material c) and (has_specified_output op some data item c and (is about op some protein domain specific binding c))) and (achieves_planned_objective op some protein and DNA interaction identification objective c)

source code modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000096

A source code module is a directive information entity that specifies, using a programming language, some algorithm.
Source
OBI_0000039
group:OBI
Example
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
has super-classes
directive information entity c

Southern blot analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000892

Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
Source
OBI & Wikipedia
Example
PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3.
has super-classes
analyte assay c
realizes op some evaluant role c and (inheres in op some high molecular weight DNA extract c)
realizes op some analyte role c and (inheres in op some scattered molecular aggregate c and (has grain op only nucleic acid c))
realizes op some complementary nucleotide probe role c and (inheres in op some nucleic acid c)
has_specified_output op some measurement datum c and (is about op some site c)
achieves_planned_objective op some assay objective c

spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000006

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
immaterial entity c
has sub-classes
one-dimensional spatial region c, three-dimensional spatial region c, two-dimensional spatial region c, zero-dimensional spatial region c
is disjoint with
site c, continuant fiat boundary c

spatiotemporal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000011

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
has super-classes
occurrent c
is disjoint with
temporal region c, process c, process boundary c

species comparison designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001310

A study design that assays differences between distinct species.
Source
MO_675 species_design
has super-classes
study design c
has part op some organism feature identification objective c
has part op some study design independent variable c and (is about op some organism c)

specific enzymatic cleavagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600050

a protocol application to digest the fraction of input material that is susceptible to that enzyme
Source
OBI branch derived
Example
The use of a protease to digest a protein into peptides
has super-classes
enzymatic cleavage c

specific labelingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600067

a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material
Source
OBI branch derived
Example
The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells
has super-classes
addition of molecular label c

specifically dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000020

A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
has super-classes
continuant c
has sub-classes
quality c, realizable entity c
is in domain of
concretizes op
is in range of
bearer of op, is concretized as op
is disjoint with
independent continuant c, generically dependent continuant c

specification of data to be generated in an investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001892

An objective specification which indicates the type of data that will be generated and submitted to a database.
Source
NIAID GSCID-BRC metadata working group
Example
Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype
has super-classes
objective specification c
part of op some study design c
is about op some data item c and (is_specified_output_of op some assay c or data transformation c)

specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100051

A material entity that has the specimen role.
Source
GROUP: OBI Biomaterial Branch
Example
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
is equivalent to
material entity c and (has role op some specimen role c)
has super-classes
material entity c
has sub-classes
bronchial alveolar lavage c, cell specimen c, cloacal specimen c, material sample c, nasal swab specimen c, nasopharyngeal aspirate specimen c, processed specimen c, specimen from organism c, specimen with known storage state c, specimen with pre- or post-mortem status c, whole organism preparation c

specimen collection objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000684

A objective specification to obtain a material entity for potential use as an input during an investigation.
Source
Bjoern Peters
Example
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has super-classes
objective specification c

specimen collection processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000659

A planned process with the objective of collecting a specimen.
Example
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
is equivalent to
planned process c and (achieves_planned_objective op some specimen collection objective c)
has super-classes
planned process c
has_specified_input op some material entity c
has_specified_output op some specimen c
has sub-classes
collecting specimen from organism c, environmental material collection process c, histological sample preparation c, material sampling process c, specimen set collection process c

specimen collection time measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001619

A time measurement datum that is the measure of the time when the specimens are collected.
Source
NIAID GSCID-BRC metadata working group
has super-classes
time measurement datum c
is about op some process boundary c and (starts op some specimen collection process c)

specimen collectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001895

A person who collects the specimen
Source
NIAID GSCID-BRC metadata working group
is equivalent to
Homo sapiens c and (has role op some specimen collector role c)
has super-classes
Homo sapiens c

specimen collector rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001769

An Investigation agent role borne by a person or organization which is realized in a specimen collection process.
Source
Penn Group
has super-classes
investigation agent role c
inheres in op some (Homo sapiens c or organization c) and (bearer of op some concretizes op some specimen collection objective c and (objective_achieved_by op some specimen collection process c and (part of op some investigation c)))

specimen containerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002088

A container with the function of containing a specimen.
Specimen containers are typically constructed or treated in a particular manner in order to perform their containing a specimen function. This will be a defined class so that any container (e.g., cryotube, vacutainer, conical test tube) with the function of containing a specimen will be inferred to be a specimen container.
Source
Duke Biobank, OBIB
Example
COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube
is equivalent to
has function op some containing a specimen function c
has super-classes
container c

specimen family creationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002095

Source
OBI, OBIB
Example
Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum.
has super-classes
material processing c
material processing c and (has_specified_input op some specimen c) and (has_specified_output op some specimens derived from shared ancestor c)

specimen fixation functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001036

a function that allows specific identification of individual speciment from one another.
Example
e.g the function of a bar code reader used to read slide bar codes
has super-classes
function c

specimen from organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001479

A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
Source
MO_954 organism_part
is equivalent to
(has role op some specimen role c) and (derives from op some material anatomical entity c or anatomical cluster c)
has super-classes
specimen c
has sub-classes
adipose tissue specimen c, adrenal gland specimen c, amniotic fluid specimen c, aorta specimen c, bile specimen c, blood specimen c, bone marrow specimen c, brain specimen c, breast specimen c, cerebellum specimen c, cerebral cortex specimen c, cerebrospinal fluid specimen c, colon specimen c, coronary artery specimen c, cortex of kidney specimen c, digestive system fluid or secretion specimen c, esophagus mucosa specimen c, esophagus muscularis mucosa specimen c, feces specimen c, hair specimen c, heart specimen c, lung specimen c, milk specimen c, pancreas specimen c, pericardial fluid specimen c, peritoneal fluid specimen c, pituitary gland specimen c, placenta specimen c, pleural fluid specimen c, prostate gland specimen c, renal medulla specimen c, saliva specimen c, sample from organism c, skeletal muscle tissue specimen c, skin of body specimen c, spleen specimen c, sputum specimen c, stomach specimen c, sweat specimen c, synovial fluid specimen c, thyroid gland specimen c, tibial artery specimen c, tibial nerve specimen c, urinary bladder specimen c, urine specimen c, vitreous humor specimen c, whole mount tissue c

specimen identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001616

A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
Source
NIAID GSCID-BRC metadata working group
has super-classes
centrally registered identifier symbol c
denotes op only specimen c
has sub-classes
specimen identifier assigned by sequencing facility c, specimen identifier assigned by specimen repository c

specimen identifier assigned by sequencing facilityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001901

A specimen identifier which is assigned by a sequencing facility
Source
NIAID GSCID-BRC metadata working group
is equivalent to
specimen identifier c and (is_specified_output_of op some assigning a centrally registered identifier c and (has participant op some sequencing facility organization c))
has super-classes
specimen identifier c

specimen identifier assigned by specimen repositoryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001900

A specimen identifier which is assigned by a specimen repository
Source
NIAID GSCID-BRC metadata working group
is equivalent to
specimen identifier c and (is_specified_output_of op some assigning a centrally registered identifier c and (has participant op some specimen repository organization c))
has super-classes
specimen identifier c

specimen provider principal investigatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001889

A person who is a principal investigator and provides the specimen
Source
NIAID GSCID-BRC metadata working group
is equivalent to
Homo sapiens c and (supplies op some specimen c) and (has role op some principal investigator role c)
has super-classes
Homo sapiens c

specimen repository organizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001885

An organization that provides a service to store and distribute specimens
Source
NIAID GSCID-BRC metadata working group
is equivalent to
organization c and (has role op some service provider role c and (realized in op some material storage service c and (has_specified_input op some specimen c)))
has super-classes
organization c

specimen rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000112

a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
Source
OBI
Example
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has super-classes
role c
inheres in op some material entity c and (is_specified_output_of op some specimen collection process c)
has sub-classes
material sample role c

specimen set collection processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002078

A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
Source
OBIB, OBI
Example
Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy.
has super-classes
specimen collection process c

specimen with known storage statec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001472

A specimen for which it is known whether it has been subjected to storage of a specified type.
Source
MO_95 BiosourceType
is equivalent to
fresh specimen c or (specimen c and (is_specified_output_of op some storage c))
has super-classes
specimen c
has sub-classes
agar stab specimen c, fresh specimen c, frozen specimen c, lyophilized specimen c, paraffin specimen c

specimen with pre- or post-mortem statusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001506

A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
Source
MO_84 OrganismStatus
is equivalent to
is_specified_output_of op some specimen collection process c and (has_specified_input op some organism c and (has quality op some alive c or dead c))
has super-classes
specimen c
has sub-classes
post mortem specimen c, pre-mortem specimen c

specimen-based scope of investigation specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001884

A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection.
Source
NIAID GSCID-BRC metadata working group
Example
Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic.
has super-classes
plan specification c
part of op some study design c
is about op some is_specified_input_of op some specimen collection process c

specimens collected in one encounterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002079

A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
Source
OBIB, OBI
Example
Both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy.
has super-classes
collection of specimens c
has sub-classes
human specimen set c

specimens collected longitudinallyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002081

A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity.
Source
Bjoern Peters, OBI
has super-classes
collection of specimens c

specimens derived from shared ancestorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002077

A collection of specimens derived from one common specimen via one or more material processing process(es).
Source
Duke Biobank, OBIB, OBI
Example
Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy.
has super-classes
collection of specimens c

SPECT scannerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001068

A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required.
Source
http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

spectrolyse heparin antifactor-Xa assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000808

A Spectrolyse Heparin (Xa) assay is intended for the quantitative determination of therapeutic Heparin in human plasma. The principle inhibitor of Thrombin, Factor Xa and other coagulation serine proteases in plasma is Antithrombin III. The rate of inhibition, under normal conditions, is slow, but can be increased several thousand-fold by Heparin. This mechanism accounts for the anticoagulant effect of Heparin. Low Molecular Weight Therapeutic Heparin (LMWH) preparations appear to catalyze the reaction between Factor Xa and Antithrombin III more readily than the reaction between Thrombin and Antithrombin III while standard Heparin catalyzes both reactions equally. The Factor Xa inhibition test is the most useful test for assaying the widest variety of therapeutic Heparin preparations. In this method, when both Factor Xa and Antithrombin III are present in excess, the rate of Factor Xa inhibition is directly proportional to the Heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the Heparin concentration.
Source
WEB:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06
Example
PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland).
has super-classes
assay c
(has_specified_input op some blood serum specimen c) and (has_specified_output op some scalar measurement datum c and (is about op some blood coagulation c))

spectrophotometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400115

A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
Source
MO
Example
Helios Gamma Spectrophotometer
has super-classes
measurement device c
has function op some measure function c
has sub-classes
LactoScope C4 c, electron paramagnetic resonance spectrometer c, fluorometer c

spectrum analysis objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200197

is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process.
Example
Calculation of characteristic path length in mass spectrometry
has super-classes
data transformation objective c

spike train datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000801

A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
Source
Jessica Turner, NIF
Example
Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
has super-classes
measurement datum c

spike-in quality control rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001140

a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes
Source
MO_937 spike_quality_control
has super-classes
reference substance role c

spin columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000570

A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232
has super-classes
chromatography column c

spinning-disk confocal microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001055

A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device.
Source
http://en.wikipedia.org/wiki/Nipkow_disk
has super-classes
confocal microscope c
has function op some measure function c

spleenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002106

the organ that functions to filter blood and to store red corpuscles and platelets
has super-classes
material anatomical entity c

spleen specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002541

A specimen that is derived from spleen.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some spleen c))
has super-classes
specimen from organism c

splenocyte specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110116

A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types.
Source
IEDB
has super-classes
processed specimen c
cell specimen c
is_specified_output_of op some organ harvesting c and (has_specified_input op some spleen c)

split-scale transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200014

A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t.
Source
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Example
This type of transformation is typically used in flow cytometry
has super-classes
data transformation c

split-ubiquitin assay c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001668

is a kind of yeast 2 hybrid system which enables membrane soluble proteins to be screened. two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (\"Cub\", residues 35–76) and an N-terminal ubiquitin moiety (\"Nub\", residues 1–34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait–prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
Source
adapted from wikipedia
Example
Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. Nikko E, André B. Eukaryot Cell. 2007 Aug;6(8):1266-77. Epub 2007 May 18. PMID: 17513562
has super-classes
binding assay c
(assay c and (has_specified_input op some genetically modified material c) and (has_specified_output op some data item c and (is about op some protein domain specific binding c))) and (achieves_planned_objective op some protein and DNA interaction identification objective c)

splitless GC injectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000525

Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent.
Source
WEB:<http://en.wikipedia.org/wiki/Gas_chromatography>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060
has super-classes
sample injection system c

sponsor rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000243

a responsible party role involved with any of the following activities: initiating, managing and funding a study
has super-classes
responsible party role c

spot cutterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001060

A robotic device that is used to excise spots from gels.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some mechanical function c

spread calculation data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200086

A spread calculation is a data transformation that has objective spread calculation.
Source
EDITOR
is equivalent to
achieves_planned_objective op some spread calculation objective c
has super-classes
data transformation c
has sub-classes
interquartile-range calculation c, kurtosis calculation c, standard deviation calculation c, variance calculation c

spread calculation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200180

is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set
Example
Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean
has super-classes
data transformation objective c

sputumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0007311

Matter ejected from the lungs, bronchi, and trachea, through the mouth.
has super-classes
organism substance c

sputum specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002508

A specimen that is derived from sputum.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some sputum c))
has super-classes
specimen from organism c

stabilization functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001041

A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity.
Example
has super-classes
function c

stainingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302887

Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
Source
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
Example
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

standard compliance rulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500024

a standard compliance rule is a compliance rule which defines conformity to a representation standard
Source
PRS
has super-classes
compliance rule c
has sub-classes
ethical standard compliance rule c

standard deviation calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200121

A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean.
Source
PERSON: Monnie McGee
has super-classes
spread calculation data transformation c
descriptive statistical calculation data transformation c
achieves_planned_objective op some descriptive statistical calculation objective c
achieves_planned_objective op some spread calculation objective c

standard errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000235

A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
Source
group:OBI
has super-classes
quantitative confidence value c

statistical hypothesis testc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000673

A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
Source
PERSON: James Malone
is equivalent to
achieves_planned_objective op some statistical hypothesis test objective c
has super-classes
data transformation c
has sub-classes
Fisher's exact test c, Student's t-test c, chi square test c

statistical hypothesis test objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000675

is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
Source
WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
has super-classes
data transformation objective c

statistical model validationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000792

A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
Source
http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29
Example
Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
is equivalent to
achieves_planned_objective op some cross validation objective c
has super-classes
partitioning data transformation c
has sub-classes
K-fold cross validation method c, boostrapping c, jackknifing method c, leave one out cross validation method c

stereo microscopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001065

An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes.
Source
http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope
has super-classes
optical microscope c
has function op some measure function c

sterilization functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000946

a function to remove viable organisms from an input material
has super-classes
function c

stimulus or stress designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001396

A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
Source
MO_568 stimulus_or_stress_design
has super-classes
intervention design c
has part op some organism feature identification objective c and (is about op some response to stimulus c)
has part op some study design independent variable c and (is about op some study intervention c)

stomachc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000945

An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
has super-classes
material anatomical entity c

stomach specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002528

A specimen that is derived from stomach.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some stomach c))
has super-classes
specimen from organism c

stopping rulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500022

a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen
Source
PRS
Example
PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy.
has super-classes
rule c

storagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302893

A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
Source
OBI-Branch
Example
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
has super-classes
material maintenance c
has_specified_input op some material entity c
achieves_planned_objective op some material maintenance objective c
has sub-classes
agar stab storage c, anticoagulant tube storage of blood specimen c, freezing storage c, lyophilization storage c, paraffin storage c

strain comparison designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001464

A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Source
MO_462 strain_or_line_design
has super-classes
study design c
has part op some organism feature identification objective c
has part op some study design independent variable c and (is about op some selectively maintained organism c)

strand of hairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001037

A filament, mostly protein, that grows from follicles found in the dermis[WP].
has super-classes
material anatomical entity c

structural analysis by paired-end tag sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001849

An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants.
Source
Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419]
Example
Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419]
has super-classes
DNA sequencing c
has part op some DNA sequencing c
has part op some paired-end library preparation c
has_specified_input op some deoxyribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some sequence feature identification objective c
has participant op some DNA sequencer c

Student's t-testc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000739

Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.
Source
WEB: http://en.wikipedia.org/wiki/T-test
has super-classes
statistical hypothesis test c
has_specified_output op some p-value c
achieves_planned_objective op some statistical hypothesis test objective c

study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500000

A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Example
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has super-classes
plan specification c
has part op some protocol c
has sub-classes
DNA methylation profiling by array design c, DNA methylation profiling by high throughput sequencing design c, RNA stability design c, RNAi profiling by array design c, all pairs design c, array platform variation design c, cell component comparison design c, cell cycle design c, cell differentiation design c, cell type comparison design c, cellular process design c, clinical history design c, clinical study design c, comparative genome hybridization by array design c, decision analysis study design c, disease state design c, dye swap design c, environmental history design c, ex vivo design c, factorial design c, family history design c, genotyping design c, hardware testing design c, imprinting design c, in vitro design c, in vivo design c, individual genetic characteristics comparison design c, injury design c, innate behavior design c, intervention design c, loop design c, matched pairs design c, normalization testing design c, observation design c, operator variation design c, operon identification design c, organism development design c, organism part comparison design c, organism status comparison design c, parallel group design c, pathogenicity design c, protein binding site identification design c, proteomic profiling by array design c, protocol optimization design c, quality control testing design c, reference design c, replicate design c, self vs self design c, sex comparison design c, species comparison design c, strain comparison design c, systematic review study design c, time series design c, transcription profiling design c, translation profiling design c, translational bias design c, validation by real time PCR design c, validation by reverse transcription PCR design c

study design controlled variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000785

Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent.
Source
WEB: http://en.wikipedia.org/wiki/Control_variable
Example
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable.
has super-classes
directive information entity c
part of op some study design c

study design dependent variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000751

dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
Source
WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
Example
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
has super-classes
directive information entity c
part of op some study design c

study design executionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000471

a planned process that carries out a study design
Source
branch derived
Example
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
is equivalent to
planned process c and (realizes op some concretizes op some study design c)
has super-classes
planned process c

study design independent variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000750

a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
Source
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
Example
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
has super-classes
directive information entity c
part of op some study design c

study group rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000174

a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
Example
The group of randomized participants that are assigned to a treatment arm of the trial
has super-classes
role c

study interventionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000931

the part of the execution of an intervention design study which is varied between two or more subjects in the study
Source
GROUP: OBI
has super-classes
planned process c
(has_specified_input op some specimen c) and (has_specified_output op some specimen c)
part of op some study design execution c and (realizes op some concretizes op some intervention design c)

sub-investigator rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000224

a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline
has super-classes
worker role c

subcutaneous injectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000954

is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe
is equivalent to
(realizes op some material to be added role c) and (realizes op some function c and (inheres in op some syringe c)) and (realizes op some target of material addition role c and (role of op some hypodermis c))
has super-classes
injection c
administering substance in vivo c
achieves_planned_objective op some adding material objective c

subgraph degree calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200138

A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph.
Source
PERSON: Richard Scheuermann
has super-classes
network subgraph quality calculation c

subgraph in-degree calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200143

A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph.
Source
PERSON: Richard Scheuermann
has super-classes
network subgraph quality calculation c

subgraph modularity calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200146

A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity.
Source
PERSON: Richard Scheuermann
has super-classes
network subgraph quality calculation c

subgraph out-degree calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200144

A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph.
Source
PERSON: Richard Scheuermann
has super-classes
network subgraph quality calculation c

subject agrees they understand informed consent documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000841

A process in which a subject receives an informed consent document and agrees that they have understood it
has super-classes
planned process c
part of op some informed consent process c

submatrix extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200074

A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.)
Source
WEB: http://en.wikipedia.org/wiki/Submatrix
Example
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set.
has super-classes
dimensionality reduction c
has sub-classes
column submatrix extraction c, row submatrix extraction c

subsetc back to ToC or Class ToC

IRI: http://www.geneontology.org/formats/oboInOwl#Subset

is equivalent to
{ core }
has super-classes
data about an ontology part c
has members
core ni

substance detectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600025

any protocol which results in the detection of a specified substance
Source
OBI branch derived
Example
the detection of phycoerytherin by means of flow cytometry
has super-classes
assay c
has_specified_input op some material entity c
has_specified_output op some measurement datum c
achieves_planned_objective op some assay objective c
has participant op some chromatography device c or gamma counter c or ion detector c or flow cytometer analyzer c or photodetector c or array scanner c or spectrophotometer c

substance unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000006

A unit which is a standardised quantity of an element or compound with uniform composition.
has super-classes
measurement unit label c
has members
micromole ni, nanomole ni, picomole ni

supercontigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000148

One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
has super-classes
sequence_assembly c

supernatant collection system harvesting framec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000146

a device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125.
Source
google
has super-classes
container c
has function op some contain function c

supernatant rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000034

supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material.
Source
OBI
Example
Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia
has super-classes
role c
inheres in op some material entity c
realized in op only material component separation c

supplementary material to a documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000326

part of a document that is segregated from the rest of the document due to its size
has super-classes
document part c

supplyingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000907

The planned process of providing material entities to be used in an investigation.
Source
Jennifer Fostel
Example
Jackson Labs supplies mouse strains.
has super-classes
planned process c
has_specified_input op some material entity c

support servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001527

A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data.
Source
PERSON; Carlo Torniai
Example
An help desk for an instrument or a software.
has super-classes
service c

support vector machinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000700

A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
Source
PERSON: Ryan Brinkman
has super-classes
class prediction data transformation c
achieves_planned_objective op some class prediction objective c
has members
GenePattern SVM ni

surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001730

A B cell epitope equilibrium association constant (KA) determination assay that uses a surface plasmon resonance assay.
Source
IEDB
is equivalent to
assay measuring the association constant [KA] of a B cell epitope:antibody complex c and (has part op some surface plasmon resonance binding assay c) and (has_specified_output op some has measurement unit label op value count per nanomolar)
has super-classes
assay measuring the association constant [KA] of a B cell epitope:antibody complex c

surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001731

A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay.
Source
IEDB
is equivalent to
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c and (has part op some surface plasmon resonance binding assay c) and (has_specified_output op some has measurement unit label op value nanomolar)
has super-classes
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex c

surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001739

A B cell epitope binding off rate measurement (koff) determination assay that uses a surface plasmon resonance assay.
Source
IEDB
is equivalent to
assay measuring the off rate [koff] of a B cell epitope:antibody complex c and (has part op some surface plasmon resonance binding assay c) and (has_specified_output op some has measurement unit label op value hertz)
has super-classes
assay measuring the off rate [koff] of a B cell epitope:antibody complex c

surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001741

A B cell epitope on rate measurement (kon) determination assay that uses a surface plasmon resonance assay.
Source
IEDB
is equivalent to
assay measuring the on rate [kon] of a B cell epitope:antibody complex c and (has part op some surface plasmon resonance binding assay c) and (has_specified_output op some has measurement unit label op value count per molar second)
has super-classes
assay measuring the on rate [kon] of a B cell epitope:antibody complex c

surface plasmon resonance binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000923

A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction.
Source
IEDB
Example
Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow.
has super-classes
binding assay c
(realizes op some function c and (inheres in op some surface plasmon resonance instrument c)) and (has_specified_input op some surface plasmon resonance instrument c)

surface plasmon resonance instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001136

A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
Source
http://en.wikipedia.org/wiki/Surface_plasmon_resonance
has super-classes
measurement device c
has function op some measure function c

surface plasmon resonance sensor chipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002046

a device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached
Source
OBI
Example
ProteOn GLC Sensor Chip #176-5011
has super-classes
device c
part of op some surface plasmon resonance instrument c
has function op some solid support function c

survival analysis data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200194

A data transformation which has the objective of performing survival analysis.
Source
PERSON: James Malone
is equivalent to
achieves_planned_objective op some survival analysis objective c
has super-classes
data transformation c
has sub-classes
Kaplan Meier c, proportional hazards model estimation c

survival analysis objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200083

A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
Source
http://en.wikipedia.org/wiki/Survival_analysis
Example
Kaplan meier data transformation
has super-classes
data transformation objective c

survival assessmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000699

Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time
has super-classes
assay c
has_specified_input op some organism c
has_specified_output op some survival rate c and (is about op some organism c)
achieves_planned_objective op some assay objective c

survival curvec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000889

A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
Source
WEB: http://www.graphpad.com/www/book/survive.htm
has super-classes
line graph c
is about op some survival rate c

survival ratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000789

A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
Source
adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
has super-classes
measurement datum c

sweatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001089

Secretion produced by a sweat gland.
has super-classes
organism substance c

sweat specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002509

A specimen that is derived from sweat.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some sweat c))
has super-classes
specimen from organism c

symbolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000028

An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
Source
based on Oxford English Dictionary
Example
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
has super-classes
information content entity c
has sub-classes
centrally registered identifier symbol c, lot number c, model number c, numeral c, serial number c, version number c

synonymc back to ToC or Class ToC

IRI: http://www.geneontology.org/formats/oboInOwl#Synonym

has super-classes
data about an ontology part c

synonym typec back to ToC or Class ToC

IRI: http://www.geneontology.org/formats/oboInOwl#SynonymType

has super-classes
data about an ontology part c

synovial fluidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001090

Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae.
has super-classes
organism substance c

synovial fluid specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002510

A specimen that is derived from synovial fluid.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some synovial fluid c))
has super-classes
specimen from organism c

synthesisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600040

the construction of a biomaterial from simpler biomaterials
Source
OBI branch derived
Example
making cDNA from nucleotides using RNA as a template
has super-classes
material processing c
has_specified_input op some molecular entity c
has_specified_output op some molecular entity c
achieves_planned_objective op some material transformation objective c

synthesizing functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000376

A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
has super-classes
function c

synthetic peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100065

a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment
Source
IEDB
Example
the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme
is equivalent to
peptide c and (is_specified_output_of op some synthesis c)
has super-classes
peptide c
processed material c

syringec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000422

a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
Source
OBI Instrument adapted from Wikipedia
Example
Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
has super-classes
device c
has function op some transfer function c

syringe filterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000543

A small membrane filter of defined pore size, that filters samples from a syringe.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122
has super-classes
chromatography detector filter c

syringe pumpc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400100

Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates.
Source
http://www.answers.com/topic/syringe, 2007-05-11
Example
NE-1000 Single Syringe Pump
has super-classes
container c
has function op some contain function c
has function op some transfer function c

Sysmex CA-6000 Coagulation Analyzerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000843

The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays
Source
web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
has super-classes
measurement device c
has function op some measure function c
is_manufactured_by op value Sysmex Corporation, Kobe, Japan

systematic review study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001958

A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed.
Example
Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/
The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/
has super-classes
study design c

T cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000084

A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
has super-classes
lymphocyte c
has sub-classes
alpha-beta T cell c

T cell activationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0042110

The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
has super-classes
biological_process c
has sub-classes
epitope specific T cell activation c

t cell epitope predictionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200060

A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope.
Source
PERSON: Helen Parkinson
has super-classes
sequence analysis data transformation c
achieves_planned_objective op some sequence analysis objective c

T cell epitope specific immune interventionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001471

An epitope specific immune intervention in which the induced response targets a T cell epitope
Source
IEDB
Example
Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide
has super-classes
epitope specific immune intervention c

T cell mediated cytotoxicityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0001913

The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
has super-classes
cell killing c
has sub-classes
epitope specific killing by T cells c

T cell proliferationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0042098

The expansion of a T cell population by cell division. Follows T cell activation.
has super-classes
cell proliferation c
has sub-classes
epitope specific T cell proliferation c

T cell receptor co-receptor CD8c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000025402

A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction.
has super-classes
protein c

T cell receptor complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0042101

A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
has super-classes
adaptive immune receptor c

T cell tolerance inductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0002517

A process involving any mechanism for tolerance induction in T cells.
has super-classes
tolerance induction c
has sub-classes
epitope specific T cell tolerance induction c

T2 cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110039

A human T-B lymphoblastoid hybrid cell line
Source
IEDB
http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1992&Template=cellBiology
has super-classes
immortal cell line c

tablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000306

A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
Example
| T F --+----- T | T F F | F F
has super-classes
textual entity c
has sub-classes
table of abbreviations c, table of contents c, table of figures c

table of abbreviationsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000307

A table where the constituent texts are abbreviations and their expansions
Example
IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
has super-classes
table c

table of contentsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000327

A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
has super-classes
table c

table of figuresc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000328

A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
has super-classes
table c

tail probability for the proportion of false positives correction methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200162

A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1.
Source
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20
has super-classes
multiple testing correction method c
achieves_planned_objective op some multiple testing correction objective c

tandem mass spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001088

A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge.
Source
http://goldbook.iupac.org/T06250.html
has super-classes
mass spectrometer c

tandem mass spectrometryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200198

Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules).
Source
PERSON: Tina Boussard
Example
A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.
has super-classes
mass spectrometry analysis c
achieves_planned_objective op some spectrum analysis objective c

target capture specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001899

A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen.
Source
NIAID GSCID-BRC metadata working group
Example
Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey
has super-classes
plan specification c
part of op some study design c
is about op some material entity c and (part of op some specimen c) and (has role op some evaluant role c and (realized in op some assay c))

target gene specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001962

is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey
Source
PRS for OBI
Example
http://www.ncbi.nlm.nih.gov/pubmed/25367129 "performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene)
has super-classes
directive information entity c

target material in specimen specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001882

A plan specification which specifies the type of material that will be assayed in an investigation.
Source
NIAID GSCID-BRC metadata working group
Example
Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome.
has super-classes
plan specification c
part of op some study design c
is about op some extract c and (is_specified_output_of op some extraction c and (has_specified_input op some specimen c))

target of material additionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110109

A material entity into which another is being added in a material combinatino process
Source
IEDB
Example
A cell culture into which a mixture of peptides is being added.
is equivalent to
has role op some target of material addition role c
has super-classes
material entity c

target of material addition rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000444

target of material addition role is a role realized by an entity into which a material is added in a material addition process
Source
OBI
Example
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
has super-classes
role c
inheres in op some material entity c
realized in op only adding a material entity into a target c

target subfragment specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001963

is a directive information specifying a genomic region, possibly located in a coding genomic region, which is the focus of a planned process such as an assay, for instance in a environmental gene survey
Source
PRS for OBI
Example
http://www.ncbi.nlm.nih.gov/pubmed/23335919 "performing a profiling of microbial phylogenetic composition using massively-parallel pyrotag sequencing targeting the V9 hypervariable region (used as target subfragment) of the 18S ribosomal RNA (rRNA) gene (used as target gene)
has super-classes
directive information entity c

taxonomic diversity assessment by targeted gene surveyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001960

is an assay which aims to provide information about taxonomic information and community diversity by mean of sequencing specific genomic regions used as marker of identity or diversity.
Source
OBI
Example
http://www.ncbi.nlm.nih.gov/pubmed/20679230 http://www.ncbi.nlm.nih.gov/pubmed/25367129
has super-classes
sequencing assay c
has_specified_output op some sequence data c and (is about op some population c)
achieves_planned_objective op some biodiversity assessment objective c

technical replicate rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000249

technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
Example
Aliquots of a tissue subjected to parallel assays
has super-classes
reference subject role c

tecmag EAGLE probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000564

The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248
has super-classes
solid NMR probe c

tecmag NMR consolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000599

An NMR console manufactured by tecmac.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246
has super-classes
NMR console c
has sub-classes
APOLLO console c, DISCOVERY console c

tecmag NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000534

An NMR instrument that is manufactured by tecmag.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250
has super-classes
NMR instrument c

temperaturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000146

A physical quality of the thermal energy of a system.
has super-classes
quality of a single physical entity c

temperature control bathc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400120

A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
Source
OBI Instrument branch
Example
VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C.
has super-classes
physical store c
has function op some contain function c
has function op some environment control function c
has sub-classes
oil bath c, water bath c

temperature unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000005

A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
has super-classes
measurement unit label c
has members
degree Celsius ni

temporal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000008

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
occurrent c
has sub-classes
one-dimensional temporal region c, zero-dimensional temporal region c
is disjoint with
spatiotemporal region c, process c, process boundary c

terbium atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33376

A lanthanoid atom that has formula Tb.
has super-classes
molecular entity c

Terbium RNA structure mapping assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001027

a single-nucleotide-resolution nucleic acid structure mapping assay which uses Terbium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Source
RNA ontology
Example
PMID:10772868
has super-classes
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing c
realizes op some reagent role c and (inheres in op some terbium atom c)
has_specified_input op some ribonucleic acid c
has_specified_output op some measurement datum c and (is about op some secondary structure of RNA molecule c)
achieves_planned_objective op some assay objective c

test substance rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000847

A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation
Source
Group:OBI
Example
fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
has super-classes
role c

test tubec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000836

A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
Source
http://en.wikipedia.org/wiki/Test_tube
has super-classes
container c
has function op some contain function c
has sub-classes
NMR sample tube c, anticoagulant-containing test tube c, cell sorter collection tube c, cytometer sample tube c, polystyrene tube c

testable hypothesisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001908

An information content entity that expresses an assertion that is intended to be tested.
Source
Group:2013 Philly Workshop group
Example
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has super-classes
information content entity c

Tet-assisted bisulfite sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002086

A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected.
Source
http://www.ncbi.nlm.nih.gov/pubmed/23196972
has super-classes
bisulfite sequencing c

Tetrapodac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_32523

has super-classes
Euteleostomi c
has sub-classes
Amniota c, Xenopus <genus> c

textual entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000300

A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
Example
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has super-classes
information content entity c
has sub-classes
caption c, citation c, comment on investigation c, conclusion textual entity c, country name c, diagnosis textual entity c, document title c, hypothesis textual entity c, institutional identification c, investigation description c, investigation title c, postal address c, sequence assembly name c, table c, written name c

thermal conductivity detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000466

The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity).
Source
WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084
has super-classes
gas chromatography detector c

thermal cyclerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400116

An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
Source
MO
Example
Piko(tm) 96-well Thermal Cycler
has super-classes
physical store c
has function op some contain function c
has function op some environment control function c
has sub-classes
PCR instrument c

thermostatic circulatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000390

A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid
Source
sep:00098
has super-classes
physical store c
has function op some contain function c
has function op some environment control function c

three dimensional cartesian spatial coordinate datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000403

A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
has super-classes
cartesian spatial coordinate datum c
denotes op some zero-dimensional spatial region c and (part of op some three-dimensional spatial region c)
has x coordinate value dp exactly 1
has z coordinate value dp exactly 1
has y coordinate value dp exactly 1

three-dimensional spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000028

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
a cube-shaped region of space
a sphere-shaped region of space,
has super-classes
spatial region c
is disjoint with
two-dimensional spatial region c, zero-dimensional spatial region c, one-dimensional spatial region c

thrombin time assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000823

A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time
Source
WEB:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06
Example
PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
has super-classes
assay c
(has_specified_input op some blood serum specimen c) and (has_specified_output op some scalar measurement datum c and (is about op some blood coagulation c))

thyroid glandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002046

A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
has super-classes
material anatomical entity c

thyroid gland specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002537

A specimen that is derived from thyroid gland.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some thyroid gland c))
has super-classes
specimen from organism c

tibial arteryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0007610

The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot.
has super-classes
material anatomical entity c

tibial artery specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002525

A specimen that is derived from tibial artery.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some tibial artery c))
has super-classes
specimen from organism c

tibial nervec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001323

The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted].
has super-classes
anatomical cluster c

tibial nerve specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002539

A specimen that is derived from tibial nerve.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some tibial nerve c))
has super-classes
specimen from organism c

tiling microarrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001307

a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions.
Source
EFO_0002704: tiling array
has super-classes
DNA microarray c
has sub-classes
Human 2.1M Whole-Genome CGH Tiling Array v2.0 c, Human 3x720K Whole Genome CGH Tiling Array c, Human 6x630K CGH Whole Genome Tiling Array c, Human Exon 1.0 ST tilling array c, Human Genome U133 Plus 2.0 tiling array c, Human Genome U133 tiling array c, Mouse 385K Whole Genome CGH Tiling Array c, Mouse 3x720K Whole Genome CGH Tiling Array c

time measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000416

A scalar measurement datum that is the result of measuring a temporal interval
has super-classes
scalar measurement datum c
(has measurement unit label op only time unit c) and (is duration of op only process c)
has sub-classes
age measurement datum c, computation run time c, half life datum (t 1/2) c, sampling time measurement datum c, specimen collection time measurement datum c
is in domain of
is duration of op
is in range of
has time stamp op

time sampled measurement data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000584

A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
Example
pmid:20604925 - time-lapse live cell microscopy
has super-classes
data set c
has part op some time stamped measurement datum c

time series designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500020

Groups of assays that are related as part of a time series.
Source
MO_887
Example
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
has super-classes
study design c

time stamped measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000582

has super-classes
measurement datum c
(has time stamp op some time measurement datum c) and (has measurement datum op some measurement datum c)
is in domain of
has measurement datum op, has time stamp op

time triggerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000034

revisit?
Source
OBI branch derived
OBI_0000331
has super-classes
conditional specification c

time unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000003

A unit which is a standard measure of the dimension in which events occur in sequence.
has super-classes
measurement unit label c
has members
day ni, hour ni, minute ni, month ni, second ni, week ni, year ni

tissuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000479

Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
has super-classes
material anatomical entity c
has sub-classes
adipose tissue c, bone marrow c, epithelium c, esophagus muscularis mucosa c, skeletal muscle tissue c

tissue embedding stationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001107

A device that is used to perform paraffin embedding of tissue specimens.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some mechanical function c

to be treated with active ingredient rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000813

A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient
Source
PERSON: Helen Parkinson
Example
Role of a patient in a group treated with an active substance in a clinical trial
has super-classes
participant under investigation role c

to be treated with placebo rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000825

A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo
has super-classes
participant under investigation role c

tolerance inductionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0002507

A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.
has super-classes
biological_process c
has sub-classes
B cell tolerance induction c, T cell tolerance induction c, epitope specific tolerance induction by T cells c

tolerance induction intervention experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001983

An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response.
Source
IEDB
Example
Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide.
has super-classes
in vivo intervention experiment c

top loading balancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001066

A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass.
Source
PERSON: Erik Segerdell
has super-classes
balance c

topologically preserved clustered data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000741

A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived.
Source
PERSON: James Malone
Example
the output data set generated from a self-organizing map.
has super-classes
clustered data set c

total intensity transformation pairedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200027

A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors).
Source
OTHER: Adjusted from MGED Ontology
Example
This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

total intensity transformation singlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200026

A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice.
Source
OTHER: Adjusted from MGED Ontology
Example
This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)).
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

total RNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000895

A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
Source
UPenn Group
Example
Extraction of total RNA from cells with Qiagen mini RNeasy kit.
has super-classes
RNA extract c
is_specified_output_of op some total RNA extraction c

total RNA extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000855

A RNA extraction process in which total cellular and organelle RNA are extracted.
Source
UPenn Group
has super-classes
RNA extraction c

TRAIL productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032639

The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

training objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000962

An training objective which is fulfilled by the provision of some training
Source
OBI
Example
A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package
has super-classes
objective specification c

training processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000939

a process that achieves a training objective
Example
e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility
is equivalent to
achieves_planned_objective op some training objective c
has super-classes
planned process c

training servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001538

A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer.
Source
PERSON: Matthew Brush
Example
A service that offers training for a specific instrument or technique. A course to learn how to use a microscope
has super-classes
service c
has part op some training process c

transcript analysis by paired-end tag sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001850

An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions.
Source
Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299]
Example
Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299]
has super-classes
transcription profiling assay c
sequencing assay c
has part op some RNA sequencing c
has part op some paired-end library preparation c
has_specified_input op some ribonucleic acid c and (has role op some evaluant role c)
has_specified_output op some DNA sequence data c
achieves_planned_objective op some transcription profiling identification objective c
has participant op some DNA sequencer c

transcript expression location detection by hybridization chain reactionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002085

An in situ hybridization in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers.
Source
PMID 21037591
Example
PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells"
has super-classes
in situ hybridization c

transcript leader sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002034

An RNA-seq assay combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing.
Source
pmid:23580730
Example
pmid:23580730
has super-classes
RNA-seq assay c

transcription cofactor activity region identification by ChIP-Seq assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002084

A ChIP-seq assay to identify regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase.
Source
FaceBase, PMID 19212405
Example
PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue"
has super-classes
ChIP-seq assay c

transcription factor binding sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000794

PLace_holder for sequence ontology term
Source
SO:0000235
has super-classes
sequence feature annotation c

transcription factor binding site assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000291

An assay with objective to find DNA region specifically recognized by proteins that function as transcription factors
Source
OBI
Example
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031
is equivalent to
assay c and (has_specified_output op some information content entity c and (is about op some transcription factor binding site c))
has super-classes
binding assay c
has_specified_output op some measurement datum c and (is about op some sequence-specific DNA binding c)
has sub-classes
transcription factor binding site identification by ChIP-Seq assay c, transcription factor binding site identification by ChIP-chip assay c

transcription factor binding site identification by ChIP-chip assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002018

A ChIP-chip assay to identify binding sites for transcription factors.
Source
Penn group
has super-classes
transcription factor binding site assay c
ChIP-chip assay c
has_specified_output op some information content entity c and (is about op some transcription factor binding site c)
achieves_planned_objective op some protein and DNA interaction identification objective c

transcription factor binding site identification by ChIP-Seq assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002019

A ChIP-seq assay to identify binding sites for transcription factors.
Source
Penn group
has super-classes
transcription factor binding site assay c
ChIP-seq assay c
has_specified_output op some information content entity c and (is about op some transcription factor binding site c)
achieves_planned_objective op some protein and DNA interaction identification objective c

transcription profiling assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000424

An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
Source
OBI
Example
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
is equivalent to
assay c and (achieves_planned_objective op some transcription profiling identification objective c)
has super-classes
analyte assay c
realizes op some analyte role c and (role of op some ribonucleic acid c)
has_specified_input op some specimen c and (has part op some ribonucleic acid c)
has_specified_output op some measurement datum c and (is about op some gene expression c)
has sub-classes
RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay c, RNA-seq assay c, cap analysis of gene expression c, microRNA profiling assay c, nano-cap analysis of gene expression c, serial analysis of gene expression c, transcript analysis by paired-end tag sequencing c, transcription profiling by MPSS assay c, transcription profiling by RT-PCR assay c, transcription profiling by array assay c, transcription profiling by tiling array assay c

transcription profiling by array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001463

An assay in which the transcriptome of a biological sample is analysed using array technology.
Source
EFO_0002768: transcription profiling by array
has super-classes
transcription profiling assay c
realizes op some analyte role c and (role of op some ribonucleic acid c)
has_specified_input op some specimen c and (has part op some ribonucleic acid c)
has_specified_output op some measurement datum c and (is about op some gene expression c)
achieves_planned_objective op some transcription profiling identification objective c
has participant op some DNA microarray c

transcription profiling by array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001290

A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
Source
MO_533 transcript_identification_design
has super-classes
transcription profiling design c
has part op some transcription profiling identification objective c
is concretized as op some realized in op some (has part op some transcription profiling by array assay c) and (has participant op some DNA microarray c)

transcription profiling by high throughput sequencing designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001239

A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance
Source
Group: ArrayExpress production team
has super-classes
transcription profiling design c
has part op some transcription profiling identification objective c
is concretized as op some realized in op some (has part op some RNA-seq assay c) and (has participant op some DNA sequencer c)

transcription profiling by MPSS assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002015

An assay in which the transcriptome of a biological sample is analysed using Massive Parallel Signature Sequencing (MPSS).
Source
http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing
has super-classes
transcription profiling assay c
has part op some DNA sequencing c
has part op some library preparation c
has_specified_output op some information content entity c and (is about op some gene expression c)
achieves_planned_objective op some transcription profiling identification objective c
has participant op some assay bead c

transcription profiling by RT-PCR assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001361

An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR)
Source
EFO_0002943: transcription profiling by RT-PCR
has super-classes
transcription profiling assay c
has part op some reverse transcribed polymerase chain reaction c
realizes op some analyte role c and (role of op some ribonucleic acid c)
has_specified_input op some specimen c and (has part op some ribonucleic acid c)
has_specified_output op some measurement datum c and (is about op some gene expression c)
achieves_planned_objective op some transcription profiling identification objective c
has participant op some PCR instrument c

transcription profiling by RT-PCR designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001313

A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
Source
Group: ArrayExpress production team
has super-classes
transcription profiling design c
has part op some transcription profiling identification objective c
is concretized as op some realized in op some (has part op some transcription profiling by RT-PCR assay c) and (has participant op some PCR instrument c)

transcription profiling by tiling array assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001235

An assay in which the transcriptome of a biological sample is analysed using a tiling path array.
Source
EFO_0002769 transcription profiling by tiling array
has super-classes
transcription profiling assay c
realizes op some analyte role c and (role of op some ribonucleic acid c)
has_specified_input op some specimen c and (has part op some ribonucleic acid c)
has_specified_output op some measurement datum c and (is about op some gene expression c)
achieves_planned_objective op some transcription profiling identification objective c
has participant op some tiling microarray c

transcription profiling by tiling array designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001427

A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.
Source
MO_507 tiling_path_design
has super-classes
transcription profiling design c
has part op some transcription profiling identification objective c
is concretized as op some realized in op some (has part op some transcription profiling by tiling array assay c) and (has participant op some tiling microarray c)

transcription profiling designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001430

A study design that identifies forms and abundance of transcripts in the genome.
Source
MO_533 transcript_identification_design
is equivalent to
(has part op some transcription profiling identification objective c) and (is concretized as op some realized in op some has part op some transcription profiling assay c)
has super-classes
study design c
has sub-classes
microRNA profiling by array design c, transcription profiling by RT-PCR design c, transcription profiling by array design c, transcription profiling by high throughput sequencing design c, transcription profiling by tiling array design c

transcription profiling identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001331

A molecular feature identification objective that aims to characterize the abundance of transcripts
Source
Group: Penn Group
has super-classes
molecular feature identification objective c
has sub-classes
transcription start site identification objective c

transcription start site identification objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001851

A transcription profiling identification objective that aims to characterize the transcription start sites of genes.
Source
Penn Group
has super-classes
transcription profiling identification objective c

transfectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001152

a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
Source
MO_366 transfection
has super-classes
genetic transformation c
has part op some cell permeabilization c
has_specified_input op some (deoxyribonucleic acid c or ribonucleic acid c) and (bearer of op some target of material addition role c)
has sub-classes
DNA transfection c

transfer functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000383

A transfer function is a function to displace a material from one location to another.
has super-classes
function c
has sub-classes
cell transfer function c, pump function c

transfer linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000572

A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system.
Source
WEB:<http://www.freepatentsonline.com/5702671.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235
has super-classes
chromatography device c

transforming growth factor beta productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071604

The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3.
has super-classes
cytokine production c
has sub-classes
epitope specific transforming growth factor-beta production by T cells c

transforming growth factor beta1 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032905

The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

transforming growth factor beta2 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032906

The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

transforming growth factor beta3 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032907

The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c

transgenic organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1000048

a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it
Source
GROUP:IEDB
Example
HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162
has super-classes
genetically modified organism c
is_specified_output_of op some genetic transformation c

translation profiling assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001282

An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
Source
EFO_0001033 translation profiling
has super-classes
analyte assay c
realizes op some analyte role c and (role of op some ribonucleic acid c)
achieves_planned_objective op some molecular feature identification objective c

translation profiling designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001410

A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
Source
Group: ArrayExpress production team
has super-classes
study design c
has part op some molecular feature identification objective c
is concretized as op some realized in op some has part op some translation profiling assay c

translation-associated transcript leader sequencingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002033

An RNA-seq assay that combines TL-seq with polysome fractionation
Source
pmid:23580730
Example
pmid:23580730
has super-classes
RNA-seq assay c

translational bias designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001259

A study design that characterizes the association of transcripts and translation machinery.
Source
MO_939 translational_bias_design
has super-classes
study design c
has part op some biological feature identification objective c

transplantationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000105

a protocol application to replace an organ or tissue of an organism
Source
OBI branch derived
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c
has sub-classes
allotransplantation c, autotransplantation c, xenotransplantation c

trap columnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000518

A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261
has super-classes
chromatography column c
has sub-classes
anion trap column c, cation trap column c

treatmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000090

A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
has super-classes
planned process c

treatment intervention experimentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001984

An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested.
Source
IEDB
Example
Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals.
has super-classes
in vivo intervention experiment c

treatment portion of study executionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000826

A planned process, part of a study design execution, during which the treatment of subjects is ongoing
has super-classes
planned process c
part of op some study design execution c
has sub-classes
single blind study execution c

trial monitor rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000060

a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
has super-classes
responsible party role c
has sub-classes
role of independent data monitoring committee c

trial statistician rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000234

a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.
has super-classes
worker role c
(has part op some realizes op some concretizes op some clinical study design c) and (realized in op only investigation c)

trisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_9754

A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
has super-classes
molecular entity c

tritiated thymidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53526

Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.
has super-classes
molecular entity c

tritiated thymidine incorporation assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000669

A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating.
Source
IEDB
Example
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity.
has super-classes
cell proliferation assay c
(realizes op some molecular label role c and (inheres in op some tritiated thymidine c)) and (has_specified_input op some tritiated thymidine c)
has part op some radioactivity detection c

trypsinationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302891

trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity
Source
OBI PA
Example
The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483
has super-classes
protease cleavage c

tumor gradingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600002

Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
Source
OBI branch derived; submitted by MO
has super-classes
assay c
has_specified_input op some specimen c
has_specified_output op some measurement datum c and (is about op some disease course c)
achieves_planned_objective op some assay objective c

tumor necrosis factor (ligand) superfamily member 11 productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0072535

The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
tumor necrosis factor superfamily cytokine production c
has sub-classes
epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells c

tumor necrosis factor productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032640

The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
tumor necrosis factor superfamily cytokine production c
has sub-classes
epitope specific TNF release by T cells c

tumor necrosis factor superfamily cytokine productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0071706

The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific tumor necrosis factor superfamily cytokine production by T cells c, lymphotoxin A production c, tumor necrosis factor (ligand) superfamily member 11 production c, tumor necrosis factor production c

two dimensional cartesian spatial coordinate datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000402

A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
has super-classes
cartesian spatial coordinate datum c
denotes op some zero-dimensional spatial region c and (part of op some two-dimensional spatial region c)
has x coordinate value dp exactly 1
has y coordinate value dp exactly 1

two-dimensional continuant fiat boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000146

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
continuant fiat boundary c
is disjoint with
one-dimensional continuant fiat boundary c, zero-dimensional continuant fiat boundary c

two-dimensional spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000009

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
has super-classes
spatial region c
is disjoint with
zero-dimensional spatial region c, one-dimensional spatial region c, three-dimensional spatial region c

two-photon laser/detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001052

A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons.
Source
http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy
has super-classes
light source c

type I interferon productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032606

The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
has super-classes
cytokine production c

type III interferon productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0034343

The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far.
has super-classes
cytokine production c

type IV hypersensitivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0001806

An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.
has super-classes
hypersensitivity c
has sub-classes
epitope specific type IV hypersensitivity by T cells c

ultrasound machinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001098

A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
Source
http://en.wikipedia.org/wiki/Sonography
has super-classes
image creation device c
has function op some image acquisition function c
has function op some measure function c

unblinding processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000840

The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials
has super-classes
planned process c
(part of op some study design execution c) and (part of op some informing subject of study arm c)

unit-variance scalingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200149

A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable.
Source
PMID:16762068
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

unplanned occurrence effecting an investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000076

a process which is external in origin to the investigation that has an impact on the outcome.
Source
OBI
Example
Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
has super-classes
process c

urinary bladderc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001255

distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
has super-classes
material anatomical entity c

urinary bladder specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002524

A specimen that is derived from urinary bladder.
Source
Chris Stoeckert, NCI BBRB
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some urinary bladder c))
has super-classes
specimen from organism c

urinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001088

Excretion that is the output of a kidney
has super-classes
organism substance c

urine specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000651

a portion of urine collected from an organism
has super-classes
specimen from organism c
is_specified_output_of op some collecting specimen from organism c
has role op some specimen role c
derives from op some urine c

vaccinationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/VO_0000002

a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response.
has super-classes
administering substance in vivo c

vaccinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/VO_0000001

A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
has super-classes
material entity c

vaccine preparationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000719

vaccine preparation is a planned process with specified output a vaccine
Source
OBI
Example
The production of B. pertussis vaccine.
has super-classes
material processing c
achieves_planned_objective op some material transformation objective c

vacuum degasserc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000495

A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily.
Source
WEB:<http://www.chromatography-online.org/topics/vacuum.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053
has super-classes
chromatography pump system c

vacuum dryerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400117

An instrument which removes liquid by the application of negative pressure, i.e. vacuum.
Source
MO
Example
Model 777 Microarray Oven
has super-classes
physical store c
has function op some contain function c
has function op some transfer function c
has function op some environment control function c

vacuum manifoldc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001116

A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY.
Source
PERSON: Erik Segerdell
has super-classes
device c
has function op some mechanical function c

vacuum ovenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001130

A device that heats materials in a vacuum.
Source
PERSON: Erik Segerdell
has super-classes
container c
environmental control device c
has function op some contain function c
has function op some heat function c
has function op some mechanical function c

validated informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302838

an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means.
Source
OBI
Example
PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..."
has super-classes
information content entity c
is_specified_output_of op some validation c

validationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302911

a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results
Source
adapted from wordnet (wkipedia)
Example
PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
has super-classes
planned process c

validation by real time PCR designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001166

a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results
Source
MO_434 real_time_PCR_quality_control
has super-classes
study design c
has part op some assay validation objective c and (objective_achieved_by op some real time polymerase chain reaction assay c)

validation by reverse transcription PCR designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001162

a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
Source
MO_986 reverse_transcription_PCR_quality_control
has super-classes
study design c
has part op some assay validation objective c and (objective_achieved_by op some reverse transcription polymerase chain reaction assay c)

value specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001933

An information content entity that specifies a value within a classification scheme or on a quantitative scale.
Example
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has super-classes
information content entity c
has sub-classes
categorical value specification c, number of errors c, scalar value specification c
is in domain of
has specified value dp, specifies value of op
is in range of
has value specification op

variable wavelength detectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000501

A chromatography detector, that can detect signals within a certain range at user-defined wavelengths.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079
has super-classes
measurement device c
has function op some measure function c

Varian GEMINI spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000477

An older Varian Broadband NMR spectrometer.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239
has super-classes
Varian NMR instrument c

Varian MERCURY spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000631

MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation.
Source
WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235
has super-classes
Varian NMR instrument c

Varian NMR instrumentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000611

An NMR instrument that is manufactured by Varian.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234
has super-classes
NMR instrument c
has sub-classes
Varian GEMINI spectrometer c, Varian MERCURY spectrometer c, Varian UNITY INOVA spectrometer c, Varian UNITY spectrometer c, Varian VXR spectrometer c

Varian UNITY INOVA spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000558

The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips.
Source
WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236
has super-classes
Varian NMR instrument c

Varian UNITY spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000579

The predecessor series of the Varian UNITY INOVA spectrometer.
Source
WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237
has super-classes
Varian NMR instrument c

Varian VXR spectrometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000524

A Varian NMR spectrometer.
Source
WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238
has super-classes
Varian NMR instrument c

variance calculationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200120

A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment.
Source
PERSON: Monnie McGee
has super-classes
spread calculation data transformation c
descriptive statistical calculation data transformation c
achieves_planned_objective op some descriptive statistical calculation objective c
achieves_planned_objective op some spread calculation objective c

variance stabilizing transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200022

A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper.
Source
PMID: 12169536
Example
This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536.
has super-classes
normalization data transformation c
achieves_planned_objective op some data normalization objective c

vascular endothelial growth factor productionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0010573

The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has super-classes
cytokine production c
has sub-classes
epitope specific vascular endothelial growth factor production by T cells c

vector mediated amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600048

The process of creating a copy of some biological entity in cell culture
Source
OBI branch derived
Example
E coli expressing the gene for M avium p35 were cultured in order to produce p35.
has super-classes
recombinant vector cloning c

vector mediated expressionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600063

vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector
Source
OBI branch derived
Example
Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity.
has super-classes
recombinant vector cloning c

veinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001638

Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
has super-classes
material anatomical entity c

Venn diagramc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000181

A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
Source
WEB: http://en.wikipedia.org/wiki/Venn_diagram
has super-classes
graph c

ventral toc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001196

A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity.
has super-classes
relational spatial quality c

versionc back to ToC or Class ToC

IRI: http://usefulinc.com/ns/doap#Version

is defined by
http://usefulinc.com/ns/doap
has super-classes
thing c

version numberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000129

A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
has super-classes
symbol c

Vertebrata <Metazoa>c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_7742

has super-classes
Bilateria c
has sub-classes
Euteleostomi c

vialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000522

A vial is a cylindrical container often made from glass tubing.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117
has super-classes
chromatography consumable c

vibration isolation tablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000945

A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor.
Source
United States Patent 6877711
has super-classes
physical store c
has function op some environment control function c

vibrotomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000959

A preparation device that uses a vibrating razor blade to cut through tissue.
has super-classes
material separation device c
has function op some material separation function c
has function op some realized in op only material component separation c

viral hemagglutination assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000871

The viral hemagglutination assay (HA) is a quantification of viruses by hemagglutination.
Source
WEB: http://en.wikipedia.org/wiki/Hemagglutination_assay
has super-classes
analyte assay c
has part op some induced hemagglutination c
has_specified_output op some measurement datum c and (is about op some Viruses c)
achieves_planned_objective op some analyte measurement objective c

viral hemagglutination inhibition assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000875

An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the antibody.
Source
Bjoern and Melanie
Example
Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody.
is equivalent to
assay c and (has_specified_input op some Viruses c) and (has_specified_output op some is about op some induced hemagglutination c)
has super-classes
assay c

viral RNA extractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000407

The extraction of RNA from an input material that specifically isolates viral RNA
Example
The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703
has super-classes
RNA extraction c
has_specified_input op some Viruses c

Virusesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10239

has super-classes
organism c

vital dye rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000221

A dye role that is realized when used to detect live cells in an experiment
Example
typtan blue has a vital dye
has super-classes
dye role c

vitreous humorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001797

transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina
has super-classes
organism substance c

vitreous humor specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002511

A specimen that is derived from vireous humor.
Source
Chris Stoeckert, Penn Medicine Biobank
is equivalent to
(specimen c and (is_specified_output_of op some collecting specimen from organism c) and (derives from op some vitreous humor c))
has super-classes
specimen from organism c

vitrification apparatusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001084

A device that is used to effect the transition of a substance into a glass.
Source
http://en.wikipedia.org/wiki/Glass_transition
has super-classes
device c
has function op some mechanical function c

voltage amplifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400101

A voltage amplifier is a device that amplifies the voltage signal.
Source
http://en.wiktionary.org/wiki/amplifier
Example
Linear amplifier, log amplifier, microwave amplifier
has super-classes
device c
has function op some signal amplification function c
has sub-classes
logarithmic voltage amplifier c, preamplifier c

voltage clamp devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001129

A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level.
Source
http://en.wikipedia.org/wiki/Voltage_clamp
has super-classes
measurement device c
has function op some measure function c

volumec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000918

A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
has super-classes
quality of a single physical entity c

volume unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000095

A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
has super-classes
measurement unit label c
has members
cubic centimeter ni, cubic decimeter ni, liter ni, microliter ni, milliliter ni, nanoliter ni, picoliter ni

volumetric flow rate unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000270

A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time .
has super-classes
measurement unit label c
has members
microliters per minute ni

vortexerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400118

A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
Source
http://en.wikipedia.org/wiki/Vortex_mixer
Example
VWR Genie 2
has super-classes
perturbation device c
has function op some perturb function c

waitingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000045

not actively doing anything to a material for a duration of time.
Source
OBI branch derived
has super-classes
exposure of material to environment c

washingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302888

washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
Source
OBI-Branch
Example
PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4.
has super-classes
material processing c
has_specified_input op some material entity c
has_specified_output op some material entity c
achieves_planned_objective op some material transformation objective c

waste tankc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400102

Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished.
Source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Example
LSR2 waste tank
has super-classes
container c
has function op some contain function c

waterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_15377

An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.
has super-classes
molecular entity c

water bathc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400155

A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
Source
PERSON: Daniel Schober
Example
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
has super-classes
temperature control bath c

weighted network graph constructionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200127

A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph.
Source
PERSON: Richard Scheuermann
has super-classes
network graph construction c

western blot analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000854

An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with antibodies specific to the analyte molecules.
Source
Philippe Rocca-Serra, IEDB
Example
Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest.
has super-classes
immunoblot assay c
(realizes op some analyte role c and (inheres in op some peptide c)) and (has_specified_input op some peptide c)

Westfall and Young family wise error rate correctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200092

Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing
has super-classes
family wise error rate correction method c
has_specified_input op some p-value c
has_specified_output op some FWER adjusted p-value c
achieves_planned_objective op some multiple testing correction objective c

whole genome sequencing assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002117

A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.
Source
http://www.ncbi.nlm.nih.gov/pubmed/25827230, http://www.ncbi.nlm.nih.gov/pubmed/23095910
Example
WGS permits comprehensive sequencing of introns and exons, whereas WES allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS/WES.
has super-classes
DNA sequencing c

whole mount tissuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1000049

A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
Source
GROUP: OBI
has super-classes
whole organism preparation c
processed specimen c
specimen from organism c
is_specified_output_of op some histological sample preparation c
derives from op some material anatomical entity c

whole organism preparationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000680

A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
Example
putting a mouse in the blender. Not: putting a mouse on a scale
has super-classes
specimen c
material entity c and (has role op some specimen role c)
is_specified_output_of op some specimen collection process c
derives from op some organism c
has sub-classes
whole mount tissue c

wild type allele informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001369

an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
Source
MO_605 genotype
has super-classes
allele information c

wild type organism genotype informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001294

a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
Source
Group: OBI group
Example
C57BL/6J wild type
has super-classes
genotype information c

worker rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000116

a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
Source
OBI
Example
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
has super-classes
investigation agent role c
has sub-classes
clinical research coordinator role c, contract research organization role c, health care provider role c, pathologist role c, proxy respondent role c, role of pathology review board c, sub-investigator role c, trial statistician role c

written namec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000590

A textual entity that denotes a particular in reality.
Source
http://code.google.com/p/information-artifact-ontology/issues/detail?id=114
Example
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
has super-classes
textual entity c
has sub-classes
author identification c

X-ray crystallography assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000912

A 3D structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest.
Source
IEDB
Example
Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes.
has super-classes
3D structure determination assay c
(realizes op some function c and (inheres in op some X-ray source c)) and (has_specified_input op some X-ray source c)

X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001738

A B cell epitope 3D structure determination assay that uses an X-ray crystallography assay.
Source
IEDB
is equivalent to
3D structure determining assay of a 3D B cell epitope:antibody complex c and (has part op some X-ray crystallography assay c) and (has_specified_output op some 3D structural organization datum c) and (has_specified_output op some has measurement unit label op value angstrom)
has super-classes
3D structure determining assay of a 3D B cell epitope:antibody complex c

X-ray crystallography assay determining the 3D structure of a MHC:ligand complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001595

A MHC binding 3D structure determination of MHC molecule:epitope complex assay that uses an X-ray crystallography assay.
Source
IEDB
is equivalent to
3D structure determining assay of a MHC:ligand complex c and (has part op some X-ray crystallography assay c) and (has_specified_input op some purified MHC molecule preparation c and (has part op some MHC protein complex c)) and (has_specified_output op some 3D structural organization datum c) and (has_specified_output op some has measurement unit label op value angstrom)
has super-classes
3D structure determining assay of a MHC:ligand complex c

X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001311

A T cell epitope 3D structure determination assay that uses an X-ray crystallography assay.
Source
IEDB
is equivalent to
3D structure determining assay of a T cell epitope:MHC:TCR complex c and (has part op some X-ray crystallography assay c) and (has_specified_output op some has measurement unit label op value angstrom)
has super-classes
3D structure determining assay of a T cell epitope:MHC:TCR complex c

X-ray sourcec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001138

A device that is used to generate X-rays.
Source
http://en.wikipedia.org/wiki/X-ray_generator
has super-classes
device c
has function op some excitation function c

xenograftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100058

A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species.
Source
WEB: http://en.wikipedia.org/wiki/Xenograft
Example
Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world
has super-classes
processed material c
is_specified_output_of op some transplantation c
derives from op some organism c

Xenopus <genus>c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_8353

has super-classes
Tetrapoda c

xenotransplantationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000043

is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
Source
OBI branch derived
has super-classes
transplantation c

y-column connectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000581

A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
Source
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237
has super-classes
column connector c

yeast 2-hybrid c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001679

yeast 2 hybrid screen is an assay meant to discover protein–protein interactions and protein–DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription.[1][2] The Y2H is thus a protein-fragment complementation assay.
Source
adapted from wikipedia
Example
Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. Reuter T, Herterich S, Bernhard O, Hoehn H, Gross HJ. Blood. 2000 Jan 15;95(2):719-20. PMID: 10627486
has super-classes
binding assay c
(assay c and (has_specified_input op some genetically modified material c) and (has_specified_output op some data item c and (is about op some protein domain specific binding c))) and (achieves_planned_objective op some protein and DNA interaction identification objective c)

yeast artificial chromosome vectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000709

a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences
has super-classes
double-stranded DNA c
cloning vector c
has role op some cloning vector role c

yeast one-hybrid c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001681

The one-hybrid variation of this technique is designed to investigate protein–DNA interactions and uses a single fusion protein in which the AD is linked directly to the binding domain.
Source
PMID: 22218861
Example
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764. PMID: 22037702
is equivalent to
(assay c and (has_specified_input op some genetically modified material c) and (has_specified_output op some data item c and (is about op some sequence-specific DNA binding c))) and (achieves_planned_objective op some assay objective c)
has super-classes
binding assay c
has sub-classes
bacterial one-hybrid c

zero-dimensional continuant fiat boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000147

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
has super-classes
continuant fiat boundary c
is disjoint with
one-dimensional continuant fiat boundary c, two-dimensional continuant fiat boundary c

zero-dimensional spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000018

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
spatial region c
is disjoint with
two-dimensional spatial region c, one-dimensional spatial region c, three-dimensional spatial region c

zero-dimensional temporal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000148

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
has super-classes
temporal region c
is disjoint with
one-dimensional temporal region c

Object Properties

2D boundary ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002000

a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
Example
the surface of my skin is a 2D boundary of my body
is inverse of
has 2D boundary op

achieves_planned_objectiveop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000417

This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
Source
PPPB branch derived
Example
A cell sorting process achieves the objective specification 'material separation objective'
has domain
planned process c
has range
objective specification c
is inverse of
objective_achieved_by op

adjacent toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002220

has sub-properties
surrounded by op

bearer ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000053

a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
Example
this apple is bearer of this red color
this vase is bearer of this fragility
has sub-properties
has function op, has quality op, has role op
has range
specifically dependent continuant c
is inverse of
inheres in op

bound_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110119

A relationship between two material entities that form a complex based on a selective, non-covalent interaction.
has domain
material entity c
has range
material entity c

browseop back to ToC or Object Property ToC

IRI: http://usefulinc.com/ns/doap#browse

is defined by
http://usefulinc.com/ns/doap

bug databaseop back to ToC or Object Property ToC

IRI: http://usefulinc.com/ns/doap#bug-database

is defined by
http://usefulinc.com/ns/doap

concretizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000059

A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
Example
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
has domain
specifically dependent continuant c
has range
generically dependent continuant c
is inverse of
is concretized as op

contains processop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000067

[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
is defined by
http://purl.obolibrary.org/obo/bfo.owl
is inverse of
occurs in op

denotesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000219

denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
Source
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
Example
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
has super-properties
is about op

derives fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001000

a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
Example
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
has super-properties
top object property
has domain
independent continuant c
has range
independent continuant c
is inverse of
derives into op

derives intoop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001001

a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
Example
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
is inverse of
derives from op

file releaseop back to ToC or Object Property ToC

IRI: http://usefulinc.com/ns/doap#file-release

is defined by
http://usefulinc.com/ns/doap

function ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000079

a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
Example
this catalysis function is a function of this enzyme
has super-properties
inheres in op
has domain
function c
is inverse of
has function op

has 2D boundaryop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002002

a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
Example
my body has 2D boundary the surface of my skin
has domain
material entity c
has range
immaterial entity c
is inverse of
2D boundary of op

has category labelop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000999

A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
has super-properties
has part op
has domain
categorical measurement datum c
has range
categorical label c

has coordinate unit labelop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000407

relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point

has characteristics: functional

has super-properties
has part op
has domain
cartesian spatial coordinate datum c
has range
length unit c

has disposition to bindop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001637

A relationship between two material entitites that each have disposition to form a complex with the other.
Source
IEDB

has characteristics: symmetric

has domain
material entity c
has range
material entity c

has functionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000085

a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
Example
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
has super-properties
bearer of op
has range
function c
is inverse of
function of op

has grainop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000643

the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Source
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
has super-properties
has part op

has measurement datumop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000583

relates a time stamped measurement datum to the measurement datum that was measured
has super-properties
has part op
has domain
time stamped measurement datum c
has range
measurement datum c and (not (time measurement datum c))

has measurement unit labelop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000039

has characteristics: functional

has super-properties
has part op
has range
measurement unit label c

has memberop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002351

has member is a mereological relation between a collection and an item.
Source
SIO

has characteristics: irreflexive

has super-properties
has part op
is inverse of
member of op

has organization memberop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001688

Relating an organization to a legal person or organization.
has domain
organization c
has range
Homo sapiens c or organization c
is inverse of
is member of organization op

has partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000051

a core relation that holds between a whole and its part
Example
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)

has characteristics: transitive

has sub-properties
has category label op, has coordinate unit label op, has grain op, has measurement datum op, has measurement unit label op, has member op, has time stamp op, has value specification op, provides_service_consumer_with op
is inverse of
part of op

has participantop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000057

a relation between a process and a continuant, in which the continuant is somehow involved in the process
Example
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
has sub-properties
has performer op, has_specified_input op, has_specified_output op
has domain
occurrent c
has range
continuant c
is inverse of
participates in op

has performerop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001950

has super-properties
has participant op
has domain
planned process c
has range
(Homo sapiens c or organization c or device c) and (has role op some investigation agent role c)

has qualityop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000086

a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
Example
this apple has quality this red color
has super-properties
bearer of op
has range
quality c
is inverse of
quality of op

has roleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000087

a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
Example
this person has role this investigator role (more colloquially: this person has this role of investigator)
has super-properties
bearer of op
has domain
independent continuant c
has range
role c
is inverse of
role of op

has time stampop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000581

relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken

has characteristics: functional

has super-properties
has part op
has domain
time stamped measurement datum c
has range
time measurement datum c

has value specificationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001938

A relation between an information content entity and a value specification that specifies its value.
Source
OBI
has super-properties
has part op
has domain
information content entity c
has range
value specification c

has_specified_inputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000293

A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Example
see is_input_of example_of_usage
has super-properties
has participant op
has domain
planned process c
is inverse of
is_specified_input_of op

has_specified_outputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000299

A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
has super-properties
has participant op
has domain
planned process c
is inverse of
is_specified_output_of op

has_supplierop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000647

A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
has domain
material entity c
has range
Homo sapiens c or organization c
is inverse of
supplies op

homepageop back to ToC or Object Property ToC

IRI: http://usefulinc.com/ns/doap#homepage

is defined by
http://usefulinc.com/ns/doap

immediately preceded byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002087

X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
has super-properties
preceded by op
has sub-properties
process is result of op
is inverse of
immediately precedes op

immediately precedesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002090

X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
has super-properties
precedes op
is inverse of
immediately preceded by op

inheres inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000052

a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
Example
this fragility inheres in this vase
this red color inheres in this apple
has sub-properties
function of op, quality of op, role of op
is inverse of
bearer of op

is aboutop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000136

is_about is a (currently) primitive relation that relates an information artifact to an entity.
Source
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
Example
This document is about information artifacts and their representations
has sub-properties
denotes op, is duration of op, is quality measurement of op, is quality specification of op, mentions op, specifies value of op
has domain
information content entity c

is concretized asop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000058

A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
Example
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
has domain
generically dependent continuant c
has range
specifically dependent continuant c
is inverse of
concretizes op

is duration ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000413

relates a process to a time-measurement-datum that represents the duration of the process
has super-properties
is about op
has domain
time measurement datum c
has range
process c

is grain ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000645

A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole.
Source
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
has super-properties
part of op

is member of organizationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000846

Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
Source
Person:Alan Ruttenberg
Person:Helen Parkinson
has domain
Homo sapiens c or organization c
has range
organization c
is inverse of
has organization member op

is quality measured asop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000417

inverse of the relation of is quality measurement of
is inverse of
is quality measurement of op

is quality measurement ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000221

m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
has super-properties
is about op
has domain
measurement datum c
has range
quality c
is inverse of
is quality measured as op

is quality specification ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000418

a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
has super-properties
is about op
is inverse of
quality is specified as op

is_manufactured_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000304

c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
Example
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
has domain
material entity c
has range
Homo sapiens c or organization c

is_proxy_forop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000314

A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
Example
position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity
has domain
continuant c
has range
continuant c

is_specified_input_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000295

A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Example
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has super-properties
participates in op
has range
planned process c
is inverse of
has_specified_input op

is_specified_output_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000312

A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
has super-properties
participates in op
has range
planned process c
is inverse of
has_specified_output op

is_supported_by_dataop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000124

The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
Source
OBI
Philly 2011 workshop
Example
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
has domain
conclusion based on data c
has range
data item c

located inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001025

a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Example
my brain is located in my head
this rat is located in this cage

has characteristics: transitive

is inverse of
location of op

location ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001015

a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Example
my head is the location of my brain
this cage is the location of this rat

has characteristics: transitive

is inverse of
located in op

mailing listop back to ToC or Object Property ToC

IRI: http://usefulinc.com/ns/doap#mailing-list

is defined by
http://usefulinc.com/ns/doap

member ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002350

is member of is a mereological relation between a item and a collection.
Source
SIO
Example
An organism that is a member of a population of organisms
has super-properties
part of op
is inverse of
has member op

mentionsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000142

An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
has super-properties
is about op

objective_achieved_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000833

This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
Source
OBI
has domain
objective specification c
has range
planned process c
is inverse of
achieves_planned_objective op

obsolete propertyop back to ToC or Object Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty

has sub-properties
obsolete_describes op, obsolete_has_function op, obsolete_has_quality op, obsolete_has_role op, obsolete_is_concretization_of op, obsolete_is_concretized_as op, obsolete_is_described_by op, obsolete_is_realized_by op, obsolete_materially denotes op, obsolete_realizes op, obsolete_represents op, obsolete_results_from op, obsolete_specifically denotes op, obsoleted_has_specified_input_information op, obsoleted_has_specified_output_information op, obsoleted_is_device_for op, obsoleted_is_reagent_in op, obsoleted_is_specified_information_intput_of op, obsoleted_is_specified_information_output_of op, obsoleted_utilizes_device op, obsoleted_utilizes_reagent op
has domain
nothing c
has range
nothing c

obsolete_describesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000222

has super-properties
obsolete property op

obsolete_has_functionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000306

Relation between an independent continuant and a function.
Example
heart has_function to-pump-blood
has super-properties
obsolete property op

obsolete_has_qualityop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000298

A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]
has super-properties
obsolete property op

obsolete_has_roleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000316

A relation between a continuant C and a role R. The reciprocal relation of role_of.
has super-properties
obsolete property op

obsolete_is_concretization_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000294

Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
has super-properties
obsolete property op

obsolete_is_concretized_asop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000297

Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
has super-properties
obsolete property op

obsolete_is_described_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110112

has super-properties
obsolete property op

obsolete_is_realized_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000300

Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
has super-properties
obsolete property op

obsolete_materially denotesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000220

has super-properties
obsolete property op

obsolete_realizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000308

Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm]
Example
example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes.
has super-properties
obsolete property op

obsolete_representsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000223

has super-properties
obsolete property op

obsolete_results_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000365

has super-properties
obsolete property op

obsolete_specifically denotesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000135

c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
Source
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
Example
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
has super-properties
obsolete property op

obsoleted_has_specified_input_informationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000315

A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.
has super-properties
obsolete property op

obsoleted_has_specified_output_informationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000301

A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.
has super-properties
obsolete property op

obsoleted_is_device_forop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000311

Relationship between a device and a protocol application in which it participates
Example
some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has super-properties
obsolete property op

obsoleted_is_reagent_inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000307

Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
Example
some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has super-properties
obsolete property op

obsoleted_is_specified_information_intput_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000644

Is the inverse relation of has_specfied_input_information
has super-properties
obsolete property op

obsoleted_is_specified_information_output_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000459

A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.
Source
Editor
has super-properties
obsolete property op

obsoleted_utilizes_deviceop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000313

Relationship between protocol application and an intrument in which it participates
Example
see example_of_usage for is_device_for
has super-properties
obsolete property op

obsoleted_utilizes_reagentop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000309

Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
Example
see example_of_usage for is_reagent_in
has super-properties
obsolete property op

occurs inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000066

b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
is defined by
http://purl.obolibrary.org/obo/bfo.owl
has domain
occurrent c
has range
independent continuant c
is inverse of
contains process op
has sub-property chains
part of op o occurs in op
occurs in op o part of op

part ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000050

a core relation that holds between a part and its whole
Example
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)

has characteristics: transitive

has sub-properties
is grain of op, member of op, starts op
is inverse of
has part op

participates inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000056

a relation between a continuant and a process, in which the continuant is somehow involved in the process
Example
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
has sub-properties
is_specified_input_of op, is_specified_output_of op
has domain
continuant c
has range
occurrent c
is inverse of
has participant op

preceded byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000062

has characteristics: transitive

has sub-properties
immediately preceded by op
has domain
occurrent c
has range
occurrent c
is inverse of
precedes op

precedesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000063

has characteristics: transitive

has super-properties
temporal relation op
has sub-properties
immediately precedes op
has domain
occurrent c
has range
occurrent c
is inverse of
preceded by op

process is result ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110060

is a relationship between a process and a preceding occurrent that directly caused the later one to occur
Example
The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
has super-properties
immediately preceded by op
has domain
occurrent c
has range
occurrent c

provides_service_consumer_withop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000107

A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
Example
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
has super-properties
has part op
has domain
service c

quality is specified asop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000419

inverse of the relation of is quality specification of
is inverse of
is quality specification of op

quality ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000080

a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
Example
this red color is a quality of this apple
has super-properties
inheres in op
is inverse of
has quality op

realized inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000054

Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
has domain
realizable entity c
has range
process c
is inverse of
realizes op

realizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000055

Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
is defined by
http://purl.obolibrary.org/obo/iao.owl
Example
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
has domain
process c
has range
realizable entity c
is inverse of
realized in op

releaseop back to ToC or Object Property ToC

IRI: http://usefulinc.com/ns/doap#release

is defined by
http://usefulinc.com/ns/doap

repositoryop back to ToC or Object Property ToC

IRI: http://usefulinc.com/ns/doap#repository

is defined by
http://usefulinc.com/ns/doap

role ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000081

a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
Example
this investigator role is a role of this person
has super-properties
inheres in op
is inverse of
has role op

specifies value ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001927

A relation between a value specification and an entity which the specification is about.
has super-properties
is about op
has domain
value specification c

startsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002223

inverse of starts with
Source
Allen
has super-properties
part of op
temporal relation op

suppliesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000646

A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
is inverse of
has_supplier op

surrounded byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002219

x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
has super-properties
adjacent to op

temporal relationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002222

A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
Source
Allen
has sub-properties
precedes op, starts op
has range
occurrent c

wikiop back to ToC or Object Property ToC

IRI: http://usefulinc.com/ns/doap#wiki

is defined by
http://usefulinc.com/ns/doap

Data Properties

has measurement valuedp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000004

has characteristics: functional

has domain
scalar measurement datum c
has range
float

has specified valuedp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001937

A relation between a value specification and a number that quantifies it.
Source
OBI
has domain
value specification c
has range
real

has x coordinate valuedp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000404

has characteristics: functional

has domain
cartesian spatial coordinate datum c
has range
float

has y coordinate valuedp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000406

has characteristics: functional

has domain
cartesian spatial coordinate datum c
has range
float

has z coordinate valuedp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000405

has characteristics: functional

has domain
cartesian spatial coordinate datum c
has range
float

has_feature_valuedp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000292

has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values.
has domain
mathematical feature c

revisiondp back to ToC or Data Property ToC

IRI: http://usefulinc.com/ns/doap#revision

is defined by
http://usefulinc.com/ns/doap

Named Individuals

ACSni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000321

ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
Source
web-page:http://www.isac-net.org/content/view/607/150/
belongs to
data format specification c

Advanced Instruments Inc. (AI Companies)ni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001375

A supplier of flow cytometry analyzers
Source
WEB:http://www.aicompanies.com/@2011/04/11
belongs to
organization c

AES Chemunexni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001428

A supplier of flow cytometry analyzers
Source
WEB:http://www.aeschemunex.com/@2011/04/11
belongs to
organization c

Affymetrixni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000462

An organization which supplies technology, tools and protocols for use in high throughput applications
belongs to
organization c

Agilentni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000765

belongs to
organization c

ambidexterousni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000979

belongs to
categorical label c

Ambionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000756

belongs to
organization c

angstromni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000019

A length unit which is equal to 10 [-10] m.
belongs to
length unit c

Antigenixni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001347

A supplier of flow cytometry analyzers
Source
WEB:http://www.antigenix.com/@2011/04/11
belongs to
organization c

Apogee Flow Systemsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001312

A supplier of flow cytometry analyzers
Source
WEB:http://www.apogeeflow.com/@2011/04/11
belongs to
organization c

Applied Biosystemsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000776

belongs to
organization c

axiom holds for all timesni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/RO_0001901

## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

Beckman Coulterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001372

A supplier of flow cytometry analyzers
Source
WEB:http://www.beckmancoulter.com/@2011/04/11
belongs to
organization c

Becton Dickinson (BD Biosciences)ni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001321

A supplier of flow cytometry analyzers
Source
WEB:http://www.bdbiosciences.com/@2011/04/11
belongs to
organization c

Bentley Instrumentsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001431

A supplier of flow cytometry analyzers
Source
WEB:http://bentleyinstruments.com/@2011/04/11
belongs to
organization c

BIO-RADni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000754

belongs to
organization c

Bruker Corporationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000770

belongs to
organization c

Bruker Daltonicsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000779

belongs to
organization c

centimeterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000015

A length unit which is equal to one hundredth of a meter or 10^[-2] m.
belongs to
length unit c

colony forming unit per volumeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000212

A concentration unit which a measure of viable bacterial numbers in a given volume.
belongs to
concentration unit c

Compensation-MLni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000329

Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
Source
web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf
belongs to
data format specification c

coreni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000224

Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
belongs to
subset c

count per molarni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000285

A rate unit which is equal to one over one molar.
belongs to
rate unit c

count per molar secondni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000282

A rate unit which is equal to one over one molar second.
belongs to
rate unit c

count per nanomolarni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000284

A rate unit which is equal to one over one nanomolar.
belongs to
rate unit c

count per nanomolar secondni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000281

A rate unit which is equal to one over one nanomolar second.
belongs to
rate unit c

cubic centimeterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000097

A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
belongs to
volume unit c

cubic decimeterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000100

A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
belongs to
volume unit c

CytoBuoyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001458

A supplier of flow cytometry analyzers
Source
WEB:http://www.cytobuoy.com/@2011/04/11
belongs to
organization c

Cytopeiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001224

A supplier of flow cytometry analyzers
Source
WEB:http://www.cytopeia.com/@2011/04/11
belongs to
organization c

Dako Cytomationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001338

A supplier of flow cytometry analyzers
Source
WEB:http://www.dakousa.com/@2011/04/11
belongs to
organization c

dayni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000033

A time unit which is equal to 24 hours.
belongs to
time unit c

defined classni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000420

A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
belongs to
denotator type c

degree Celsiusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000027

A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
belongs to
temperature unit c

eBioscienceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001213

A supplier of flow cytometry analyzers
Source
WEB:http://www.ebioscience.com/@2011/04/11
belongs to
organization c

Edingburgh handedness inventoryni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001004

The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
Source
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
belongs to
questionnaire c

Exalpha Biologicalni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001287

A supplier of flow cytometry analyzers
Source
WEB:http://www.exalpha.com/@2011/04/11
belongs to
organization c

example to be eventually removedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000002

belongs to
curation status specification c

Exbio Antibodiesni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001320

A supplier of flow cytometry analyzers
Source
WEB:http://www.exbio.cz/@2011/04/11
belongs to
organization c

FCSni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000327

FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
Source
web-page:http://www.fcspress.com/
belongs to
data format specification c

Gating-MLni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000330

Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
Source
web-page:http://www.flowcyt.org/gating/
belongs to
data format specification c

GenePattern CARTni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000767

belongs to
CART c

GenePattern HeatMapViewer data visualizationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000780

The GenePattern process of generating Heat Maps from clustered data.
belongs to
clustered data visualization c

GenePattern hierarchical clusteringni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000755

belongs to
hierarchical clustering c

GenePattern HierarchicalClusteringViewer data visualizationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000781

The GenePattern process of generating hierarchical clustering visualization from clustered data.
belongs to
clustered data visualization c

GenePattern k-means clusteringni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000764

belongs to
k-means clustering c

GenePattern k-nearest neighborsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000762

belongs to
k-nearest neighbors c

GenePattern LOOCVni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000763

belongs to
leave one out cross validation method c

GenePattern module CARTXValidationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000768

GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
belongs to
GenePattern software c
has facts
is about op GenePattern LOOCV
is about op GenePattern CART

GenePattern module HeatMapViewerni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000782

A GenePattern software module which is used to generate a heatmap view of data.
belongs to
GenePattern software c
has facts
is about op GenePattern HeatMapViewer data visualization

GenePattern module HierarchicalClusteringni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000774

GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
belongs to
GenePattern software c
has facts
is about op GenePattern hierarchical clustering

GenePattern module HierarchicalClusteringViewerni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000783

A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
belongs to
GenePattern software c
has facts
is about op GenePattern HierarchicalClusteringViewer data visualization

GenePattern module KMeansClusteringni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000766

GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
Source
PERSON: James Malone
belongs to
GenePattern software c
has facts
is about op GenePattern k-means clustering

GenePattern module KNNni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000773

GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
belongs to
GenePattern software c
has facts
is about op GenePattern k-nearest neighbors

GenePattern module KNNXValidationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000771

GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
Source
PERSON: James Malone
belongs to
GenePattern software c

GenePattern module PCAni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000777

GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
Source
PERSON: James Malone
belongs to
GenePattern software c
has facts
is about op GenePattern PCA

GenePattern module PeakMatchni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000772

belongs to
GenePattern software c
has facts
is about op GenePattern peak matching

GenePattern module SVMni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000761

GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
belongs to
GenePattern software c
has facts
is about op GenePattern SVM

GenePattern PCAni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000760

belongs to
principal components analysis dimensionality reduction c

GenePattern peak matchingni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000778

belongs to
peak matching c

GenePattern SVMni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000775

belongs to
support vector machine c

gramni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000021

A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
belongs to
mass unit c

gram per deciliterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000208

A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
belongs to
concentration unit c

gram per literni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000175

A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
belongs to
concentration unit c

Helicosni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000757

belongs to
organization c

hertzni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000106

A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
belongs to
frequency unit c

hourni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000032

A time unit which is equal to 3600 seconds or 60 minutes.
belongs to
time unit c

Illuminani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000759

belongs to
organization c

Invitrogenni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001434

A supplier of flow cytometry analyzers
Source
WEB:http://www.invitrogen.com/@2011/04/11
belongs to
organization c

kilogramni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000009

A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
belongs to
mass unit c

left handedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000998

belongs to
categorical label c

Li-Corni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000769

belongs to
organization c

literni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000099

A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
belongs to
volume unit c

Luminexni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001443

A supplier of flow cytometry analyzers
Source
WEB:http://www.luminexcorp.com/@2011/04/11
belongs to
organization c

mass percentageni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000163

A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
belongs to
concentration unit c

mass volume percentageni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000164

A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
belongs to
concentration unit c

meterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000008

A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
belongs to
length unit c

microgramni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000023

A mass unit which is equal to one millionth of a gram or 10^[-6] g.
belongs to
mass unit c

microgram per literni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000301

A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
belongs to
concentration unit c

microliterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000101

A volume unit which is equal to one millionth of a liter or 10^[-6] L.
belongs to
volume unit c

microliters per minuteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000271

A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
belongs to
volumetric flow rate unit c

micrometerni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000017

A length unit which is equal to one millionth of a meter or 10^[-6] m.
belongs to
length unit c

micromolarni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000064

A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
belongs to
concentration unit c

micromoleni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000039

A substance unit equal to a millionth of a mol or 10^[-6] mol.
belongs to
substance unit c

milligramni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000022

A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
belongs to
mass unit c

milligram per milliliterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000176

A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
belongs to
concentration unit c

milliliterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000098

A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
belongs to
volume unit c

milliliter per literni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000207

A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
belongs to
concentration unit c

millimeterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000016

A length unit which is equal to one thousandth of a meter or 10^[-3] m.
belongs to
length unit c

millimolarni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000063

A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
belongs to
concentration unit c

Milliporeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001340

A supplier of flow cytometry analyzers
Source
WEB:http://www.guavatechnologies.com/@2011/04/11
belongs to
organization c

Miltenyi Biotecni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001424

A supplier of flow cytometry analyzers
Source
WEB:http://www.miltenyibiotec.com/@2011/04/11
belongs to
organization c

minuteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000031

A time unit which is equal to 60 seconds.
belongs to
time unit c

molarni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000062

A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
belongs to
concentration unit c

monthni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000035

A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
belongs to
time unit c

named class expressionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000421

A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
belongs to
denotator type c

nanogramni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000024

A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
belongs to
mass unit c

nanoliterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000102

A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
belongs to
volume unit c

nanometerni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000018

A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
belongs to
length unit c

nanomolarni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000065

A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
belongs to
concentration unit c

nanomoleni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000041

A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
belongs to
substance unit c

NanoString Technologiesni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001860

An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
belongs to
organization c

Nimblegenni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001855

An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
belongs to
organization c

otherni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000230

belongs to
obsolescence reason specification c

OWLni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000332

OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
Source
web-page:http://www.w3.org/2004/OWL/
belongs to
data format specification c

Pacific Biosciencesni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001856

An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
belongs to
organization c

Partecni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001355

A supplier of flow cytometry analyzers
Source
WEB:http://www.partec.de/@2011/04/11
belongs to
organization c

pHni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000196

A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
belongs to
concentration unit c

picogramni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000025

A mass unit which is equal to 10^[-12] g.
belongs to
mass unit c

picoliterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000103

A volume unit which is equal to 10^[-12] L.
belongs to
volume unit c

picomolarni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000066

A unit of molarity which is equal to 10^[-12] M.
belongs to
concentration unit c

picomoleni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000042

A substance unit equal to 10^[-12] mol.
belongs to
substance unit c

projectni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/iao/project

belongs to
project c
has facts
bug database op tracker
homepage op iao
mailing list op mailto:information-ontology@googlegroups.com
release op IAO Release 2015-02-23
repository op repository
wiki op documentation

projectni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/obi/project

belongs to
project c
has facts
browse op browse
bug database op tracker
homepage op obi
mailing list op mailto:obi-users@googlegroups.com
release op OBI Release 2016-10-11
repository op repository
wiki op wiki

RDFni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000324

RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
Source
web-page:http://www.w3.org/RDF/
belongs to
data format specification c

relation has no temporal argumentni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/RO_0001902

## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)

repositoryni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/iao/repository

belongs to
s v n repository c

repositoryni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/obi/repository

belongs to
s v n repository c

requires discussionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000428

A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Source
group:OBI
belongs to
curation status specification c

right handedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000958

belongs to
categorical label c

Rocheni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000758

belongs to
organization c

secondni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000010

A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
belongs to
time unit c

Sysmex Corporation, Kobe, Japanni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000829

Source
WEB:http://www.sysmex.com/@2009/08/06
belongs to
organization c

tarni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000326

tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
Source
web-page:http://www.gnu.org/software/tar/manual/
belongs to
data format specification c

term importedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000228

belongs to
obsolescence reason specification c

term splitni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000229

belongs to
obsolescence reason specification c

terms mergedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000227

belongs to
obsolescence reason specification c

Thermoni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000752

belongs to
organization c

to be replaced with external ontology termni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000423

Terms with this status should eventually replaced with a term from another ontology.
Source
group:OBI
belongs to
curation status specification c

Transformation-MLni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000317

Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
Source
web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf
belongs to
data format specification c

U.S. Food and Drug Administrationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000901

belongs to
organization c

universalni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000410

Source
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
belongs to
denotator type c

volume percentageni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000165

A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
belongs to
concentration unit c

Watersni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000753

belongs to
organization c

weekni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000034

A time unit which is equal to 7 days.
belongs to
time unit c

XMLni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000322

XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
Source
web-page:http://www.w3.org/XML/
belongs to
data format specification c

yearni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000036

A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
belongs to
time unit c

zipni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000325

zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
Source
web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/
belongs to
data format specification c

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals